Mercurial > repos > pieterlukasse > prims_metabolomics

comparison msclust.xml @ 4:80075a4c6543

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updated image paths
author pieter.lukasse@wur.nl
date Fri, 17 Jan 2014 12:43:05 +0100
parents 2c1c9f0d8aa6
children 64380b35b8a6
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3:2c1c9f0d8aa6 4:80075a4c6543
195 195
196 This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and 196 This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and
197 retention times of the putative ions to cluster them. Each cluster is then used to generate 197 retention times of the putative ions to cluster them. Each cluster is then used to generate
198 one spectrum containing the clustered ions (peaks). 198 one spectrum containing the clustered ions (peaks).
199 199
200 .. image:: $PATH_TO_IMAGES/msclust_summary.png 200 .. image:: msclust_summary.png
201 201
202 202
203 ----- 203 -----
204 204
205 **Output** 205 **Output**
235 values = stricter separation at the value determined in 'Potential Density reduction' above 235 values = stricter separation at the value determined in 'Potential Density reduction' above
236 (TODO review this comment). 236 (TODO review this comment).
237 237
238 *Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations 238 *Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations
239 239
240 .. __: javascript:window.open('$PATH_TO_IMAGES/confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes') 240 .. __: javascript:window.open('confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
241 241
242 242
243 ----- 243 -----
244 244
245 **Output files described below** 245 **Output files described below**
248 248
249 *SPECTRA:* this file can be submitted to NIST for identification of the spectra. 249 *SPECTRA:* this file can be submitted to NIST for identification of the spectra.
250 250
251 `Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_ 251 `Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_
252 252
253 .. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('$PATH_TO_IMAGES/sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes') 253 .. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
254 254
255 ----- 255 -----
256 256
257 *MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count 257 *MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count
258 values (corrected by their membership) for all MEASURED cluster ions in the given sample. 258 values (corrected by their membership) for all MEASURED cluster ions in the given sample.
279 by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not 279 by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not
280 "shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. 280 "shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file.
281 281
282 `Click here for more details on the SIM output file`_ 282 `Click here for more details on the SIM output file`_
283 283
284 .. _Click here for more details on the SIM output file: javascript:window.open('$PATH_TO_IMAGES/sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes') 284 .. _Click here for more details on the SIM output file: javascript:window.open('sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
285 285
286 286
287 287
288 </help> 288 </help>
289 </tool> 289 </tool>