annotate preprocess_datasets/Affymetrix.Rmd @ 46:31f89047724f draft default tip

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author proteomisc
date Mon, 29 Jan 2024 09:34:13 +0000
parents 8aaf6fdb06d6
children
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1 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="fr" lang="fr"><head>
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2 <meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
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3 <title>Preprocessing Plots Before and After</title>
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4 <style>
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5 /* css racine */
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6
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7 body {
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8 /* font-family: Comic Sans MS;*/
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9 }
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10
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11 div.research {
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12 background-color: #33ffff; /*#208090 */ /*#228491*/;
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13 color: #0000ff; /* ffffff */
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14 }
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15
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16 div.ensg {
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17 background-color: #bbee00;
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18 color: #0000ff;
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19 }
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20
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21 div.research span.invisible {
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22 visibility:hidden;
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23 }
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24
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25 kbd {
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26 color: #000000;
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27 }
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28
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29 pre {
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30 color: #000000;
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31 }
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32
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33 A:link {
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34 color: #0000ee; /*#ffffff;*/
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35 }
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36
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37 A:active {
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38 color: #ff0000; /* #ffffff */
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39 }
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40
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41 A:hover {
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42 /* font-size: 2em; */
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43 text-decoration: none;
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44 color: #0000ee; /* ffffff */
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45 background-color: #FFFF33;
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46 }
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47
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48 h3 {
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49 color: #FF0000;
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50 }
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51
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52 h4 {
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53 color: #FF0000;
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54 }
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55
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56 div.correction {
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57 color: #008800;
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58 /* color: #000000; */
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59 }
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60
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61 div.detail {
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62 font-size: 70%;
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63 }
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64
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65 div.section {
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66 text-align: center;
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67 font-size: 140%;
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68 color: #FF0000;
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69 }
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70
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71 div.subsection {
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72 text-align: left;
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73 font-size: 120%;
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74 color: #bb0000;
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75 background-color: #FFFF33;
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76 }
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77
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78 div.titreDuModule {
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79 text-align: center;
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80 font-size: 200%;
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81 color: #FF0099;
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82 }
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83
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84 div.formation {
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85 text-align: center;
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86 font-size: 120%;
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87 color: #FF0099;
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88 }
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89
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90 div.ensg.titreDuModule {
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91 text-align: center;
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92 font-size: 200%;
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93 color: #FF0099;
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94 }
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95
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96 div.ensg.formation {
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97 text-align: center;
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98 font-size: 120%;
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99 color: #FF0099;
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100 }
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101
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102 span.indice {
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103 font-size: 70%;
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104 }
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105
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106 span.question {
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107 color: #bb0000;
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108 }
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109
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110 span.tresImportant {
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111 color: #bb0000;
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112 font-size: 200%
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113 }
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114
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115 span.assezImportant {
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116 color: #bb0000;
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117 font-size: 150%
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118 }
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119
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120 span.important {
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121 color: #bb0000;
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122 }
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123
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124 span.crucial {
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125 color: #bb0000;
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126 }
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127
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128 span.crucial:hover {
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129 font-size: 400%;
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130 }
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131
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132 acronym {
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133 text-decoration: none;
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134 }
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135
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136 div.theoreme:before {
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137 content: "Théorème : ";
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138 }
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139
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140 div.theoreme:after {
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141 content: "emèroéhT";
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142 }
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143
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144 div.theoreme ul li:before {
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145 content: "1 alinéa ";
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146 }
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147
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148 div.theoreme li:after {
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149 content: " ce qui termine l'alinéa";
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150 }
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151
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152 div.tpID {
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153 background-color: #33ffff;
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154 color: #0000ff;
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155 }
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156
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157 div.tpR {
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158 font-family: serif;
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159 color: #000000;
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160 background-color: #fff;
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161 }
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162
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163 div.tpR span.detail {
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164 font-size: 75%;
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165 }
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166
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167 div.tpR div.correction:before {
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168 content: "Idée de la correction : ";
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169 }
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170
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171 div.tpR div.correction {
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172 background-color: #00ffff;
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173 border: solid #009999;
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174 padding: 0.5em;
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175 margin-left: 2em;
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176 border-width: 1px;
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177 }
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178
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179 div.tpR div.exercices:before {
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180 content: "Exercices : ";
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181 }
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182 div.tpR div.exercices {
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183 background-color: #00ee00;
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184 border: solid #00cc00;
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185 padding: 0.5em;
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186 margin-left: 2em;
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187 border-width: 1px;
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188 }
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189
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190 div.tpR div.solution:before {
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191 content: "Solution : ";
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192 }
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193 div.tpR div.solution {
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194 background-color: #ff00ff;
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195 border: solid #990099;
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196 padding: 0.5em;
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197 margin-left: 2em;
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198 border-width: 1px;
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199 }
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200
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201 div.tpR div.exercice:before {
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202 content: "Exercice : ";
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203 }
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204 div.tpR div.exercice {
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205 background-color: #00ee00;
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206 border: solid #00cc00;
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207 padding: 0.5em;
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208 margin-left: 2em;
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209 border-width: 1px;
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210 }
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211
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212 div.tpR div.questions:before {
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213 content: "Questions : ";
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214 }
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215 div.tpR div.questions {
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216 background-color: #ff99ff;
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217 border: solid #ff99ff;
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218 padding: 0.5em;
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219 margin-left: 2em;
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220 border-width: 1px;
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221 }
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222
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223 div.tpR span.index {
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224 /* background-color: #ffff33;*/
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225 }
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226
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proteomisc
parents:
diff changeset
227 div.tpR h1 {
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proteomisc
parents:
diff changeset
228 font-family: sans-serif;
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proteomisc
parents:
diff changeset
229 color: #000;
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proteomisc
parents:
diff changeset
230 border-style: solid;
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proteomisc
parents:
diff changeset
231 background-color: #ddf;
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proteomisc
parents:
diff changeset
232 border-color: #88f;
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proteomisc
parents:
diff changeset
233 border-width: 1px;
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proteomisc
parents:
diff changeset
234 padding-left: 0.5em;
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proteomisc
parents:
diff changeset
235 }
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proteomisc
parents:
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236
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proteomisc
parents:
diff changeset
237 div.tpR h2 {
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proteomisc
parents:
diff changeset
238 font-family: sans-serif;
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proteomisc
parents:
diff changeset
239 color: #000;
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proteomisc
parents:
diff changeset
240 border-style: solid;
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proteomisc
parents:
diff changeset
241 border-color: #8f8;
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proteomisc
parents:
diff changeset
242 background-color: #dfd;
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proteomisc
parents:
diff changeset
243 border-width: 1px;
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proteomisc
parents:
diff changeset
244 padding-left: 0.5em;
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proteomisc
parents:
diff changeset
245 }
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proteomisc
parents:
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246
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proteomisc
parents:
diff changeset
247 div.tpR h3 {
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proteomisc
parents:
diff changeset
248 font-family: sans-serif;
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proteomisc
parents:
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249 color: #000;
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proteomisc
parents:
diff changeset
250 border-style: solid;
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proteomisc
parents:
diff changeset
251 background-color: #fdd;
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proteomisc
parents:
diff changeset
252 border-color: #f88;
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proteomisc
parents:
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253 border-width: 1px;
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proteomisc
parents:
diff changeset
254 padding-left: 0.5em;
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proteomisc
parents:
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255 }
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proteomisc
parents:
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256
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proteomisc
parents:
diff changeset
257 div.tpR a:link {
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proteomisc
parents:
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258 color: #00f
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proteomisc
parents:
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259 }
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proteomisc
parents:
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260
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proteomisc
parents:
diff changeset
261 div.tpR a:visited {
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proteomisc
parents:
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262 color: #f0f
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proteomisc
parents:
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263 }
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proteomisc
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264
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proteomisc
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265 div.tpR p {
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proteomisc
parents:
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266 margin-left: 1em;
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proteomisc
parents:
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267 }
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proteomisc
parents:
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268
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proteomisc
parents:
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269 div.tpR pre {
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proteomisc
parents:
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270 background-color: #eee;
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proteomisc
parents:
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271 border: solid #ccc;
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proteomisc
parents:
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272 padding: 0.5em;
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proteomisc
parents:
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273 margin-left: 2em;
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proteomisc
parents:
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274 border-width: 1px;
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proteomisc
parents:
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275 }
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proteomisc
parents:
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276
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proteomisc
parents:
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277 .redify pre {
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proteomisc
parents:
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278 color: #ff0000;
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proteomisc
parents:
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279 }
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proteomisc
parents:
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280
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proteomisc
parents:
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281 div.tpR hr {
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proteomisc
parents:
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282 border-style: solid;
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proteomisc
parents:
diff changeset
283 border-color: #02c;
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proteomisc
parents:
diff changeset
284 background-color: #ddf;
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proteomisc
parents:
diff changeset
285 border-color: #88f;
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proteomisc
parents:
diff changeset
286 border-width: 1px;
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proteomisc
parents:
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287 padding-top: 1px;
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proteomisc
parents:
diff changeset
288 padding-bottom: 1px;
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proteomisc
parents:
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289 }
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proteomisc
parents:
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290
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proteomisc
parents:
diff changeset
291 div.pp {
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proteomisc
parents:
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292 color: #FF0000;
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proteomisc
parents:
diff changeset
293 }
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proteomisc
parents:
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294
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proteomisc
parents:
diff changeset
295 div.infobulle{
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proteomisc
parents:
diff changeset
296 position: absolute;
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proteomisc
parents:
diff changeset
297 visibility : hidden;
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proteomisc
parents:
diff changeset
298 border: 1px solid Black;
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proteomisc
parents:
diff changeset
299 padding: 10px;
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proteomisc
parents:
diff changeset
300 font-family: Verdana, Arial;
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proteomisc
parents:
diff changeset
301 font-size: 13px;
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proteomisc
parents:
diff changeset
302 background-color: #ffffff;
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proteomisc
parents:
diff changeset
303 -moz-border-radius: 20px; /* pour avoir des coins arrondis */
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proteomisc
parents:
diff changeset
304 }
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proteomisc
parents:
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305
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proteomisc
parents:
diff changeset
306 /* http://www.w3schools.com/CSS/css_display_visibility.asp */
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proteomisc
parents:
diff changeset
307 span.commentPub{
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proteomisc
parents:
diff changeset
308 background-color: #77ff33;
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proteomisc
parents:
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309 }
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proteomisc
parents:
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310
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proteomisc
parents:
diff changeset
311 span.moreCommentOnPub{
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proteomisc
parents:
diff changeset
312 /* position: absolute;*/
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proteomisc
parents:
diff changeset
313 /* visibility : hidden;*/
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proteomisc
parents:
diff changeset
314 /* border: 1px solid Black;
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proteomisc
parents:
diff changeset
315 padding: 10px;
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proteomisc
parents:
diff changeset
316 font-family: Verdana, Arial;
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proteomisc
parents:
diff changeset
317 font-size: 13px;*/
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proteomisc
parents:
diff changeset
318 background-color: #77ff33;
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proteomisc
parents:
diff changeset
319 -moz-border-radius: 3em 1em /* 20px; pour avoir des coins arrondis */
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proteomisc
parents:
diff changeset
320 border-radius: 3em 1em; /* 20px; pour avoir des coins arrondis */
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proteomisc
parents:
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321 }
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proteomisc
parents:
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322 </style>
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proteomisc
parents:
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323 </head>
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proteomisc
parents:
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324 <body>
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proteomisc
parents:
diff changeset
325 <div class="tpR">
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proteomisc
parents:
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326 <h1>Preprocessing</h1>
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proteomisc
parents:
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327 <p>
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proteomisc
parents:
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328 Preprocessing of an `r datasetsource` DataSet, issued from
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proteomisc
parents:
diff changeset
329 `r technology`
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proteomisc
parents:
diff changeset
330 technology.
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proteomisc
parents:
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331 </p>
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proteomisc
parents:
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332 <h2>Used methods for each step</h2>
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proteomisc
parents:
diff changeset
333
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proteomisc
parents:
diff changeset
334 <h3>Background correction methods</h3>
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proteomisc
parents:
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335 <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
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proteomisc
parents:
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336 <h3>Normalization methods</h3>
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proteomisc
parents:
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337 <pre>method : `r listArguments[["normalization_method"]]`</pre>
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proteomisc
parents:
diff changeset
338 <h3>Summarization methods</h3>
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proteomisc
parents:
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339 <pre>method : `r listArguments[["summary_method"]]`</pre>
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proteomisc
parents:
diff changeset
340 <h2>Boxplots</h2>
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proteomisc
parents:
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341 <h3>Before NM</h3>
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proteomisc
parents:
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342 <p>
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proteomisc
parents:
diff changeset
343 <br>
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proteomisc
parents:
diff changeset
344 <img src="boxplot_before_NM.png" width="100%" height="auto">
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proteomisc
parents:
diff changeset
345 <br>
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proteomisc
parents:
diff changeset
346 </p>
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proteomisc
parents:
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347 <h3>After NM</h3>
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proteomisc
parents:
diff changeset
348 <p>
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proteomisc
parents:
diff changeset
349 <br>
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proteomisc
parents:
diff changeset
350 <img src="boxplot_after_NM.png" width="100%" height="auto">
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proteomisc
parents:
diff changeset
351 <br>
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proteomisc
parents:
diff changeset
352 </p>
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proteomisc
parents:
diff changeset
353 <h2>MA plots</h2>
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proteomisc
parents:
diff changeset
354 <p>
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proteomisc
parents:
diff changeset
355 <br>
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proteomisc
parents:
diff changeset
356 <img src="MA_plot.png" width="100%" height="auto">
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proteomisc
parents:
diff changeset
357 <br>
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proteomisc
parents:
diff changeset
358 </p>
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proteomisc
parents:
diff changeset
359 <h2>Densities plot</h2>
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proteomisc
parents:
diff changeset
360 <h3>Before NM</h3>
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proteomisc
parents:
diff changeset
361 <p>
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proteomisc
parents:
diff changeset
362 <br>
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proteomisc
parents:
diff changeset
363 <img src="densities_plot_before_NM.png" width="100%" height="auto">
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proteomisc
parents:
diff changeset
364 <br>
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proteomisc
parents:
diff changeset
365 </p>
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proteomisc
parents:
diff changeset
366 <h3>After NM</h3>
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proteomisc
parents:
diff changeset
367 <p>
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proteomisc
parents:
diff changeset
368 <br>
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proteomisc
parents:
diff changeset
369 <img src="densities_plot_after_NM.png" width="100%" height="auto">
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proteomisc
parents:
diff changeset
370 <br>
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proteomisc
parents:
diff changeset
371 </p>
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proteomisc
parents:
diff changeset
372 </body>
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proteomisc
parents:
diff changeset
373 </html>