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comparison EBIsoformTwoCondTest.xml @ 16:7218b8ff560e draft

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author ning
date Fri, 15 Mar 2013 18:56:03 -0400
parents cd0637465b05
children b2462f571961
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15:58bb88f53765 16:7218b8ff560e
25 <help> 25 <help>
26 The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the isoform names column). 26 The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the isoform names column).
27 27
28 The Ig Vector could be generated by the GetIg function or obtained from RSEM output. 28 The Ig Vector could be generated by the GetIg function or obtained from RSEM output.
29 29
30 Four output files will be generated. Each file contains Posterior probability of being DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized isoform expressions. 30 Four output files will be generated. Each of the first 3 files contains Posterior probability of being DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized isoform expressions.
31 The four files are: 31 The four files are:
32 32
33 Isoforms with the same order as in input file; 33 Isoforms with the same order as in input file;
34 Isoforms sorted by PPDE; DE Isoforms under target FDR (PPDE>=TargetFDR) 34 Isoforms sorted by PPDE; DE Isoforms under target FDR (PPDE>=TargetFDR)
35 and sorted by PPDE. 35 and sorted by PPDE;
36 Library size factor for each sample. 36 Library size factor for each sample.
37 37
38 </help> 38 </help>
39 39
40 40