Gene-Level SAM

This script is designed to generate SAM (Tusher, et al., 2001) results in the gene-level. SAM t-statistics at the probeset-level are collapsed into the gene-level by using the highest absolute value.
Usage: Rscript gene_sam.r [input file] [response type] [gene-level expression value] [fold-change value] [SAM statistic value]
Example: Rscript gene_sam.r GSE14407.csv "Two class unpaired" GSE14407_xg.csv GSE14407_foldchange.csv GSE14407_samt.csv

Response types

One class
Two class unpaired
Two class paired
Multiclass
Quantitative
Survival
One class timecourse
Two class unpaired timecourse
Two class paired timecourse
Pattern discovery

Input

ID_REF,GSM397626,GSM397627,GSM397628,...
,2,2,2,...
1007_s_at,1064.522986,1257.175612,529.2437438,...
1053_at,271.0455304,472.0113,230.9577961,...
117_at,332.520232,545.0578175,15.41981546,...

Output

gene-level expression

ID_REF,GSM397626,GSM397627,GSM397628,...
,2,2,2,...
"1",22.67582246,39.61035206,47.58530678,...
"10",15.41437907,12.07715154,14.21503508,...
"100",955.6461009,1139.522291,485.2423776,...

fold-change

1,0.342782008880577
10,-0.368245020994304
100,-1.29034936117725
...

SAM statistic

1,0.613540751874481
10,-3.87826907460695
100,-3.04801738865691
...

Last edited Feb 7, 2013 at 10:25 PM by yongkeecho, version 5

Comments

No comments yet.