i am using EMA package for mining gene expression data , i need to get list of gene expression. here is some of code: > rbasalt <- runTtest(basalt, blabelt,typeFDR="FDR-BH",algo="t", q=0.01, plot=TRUE) Launch t test Calculate pval Adjusted pval [1] "typeFDR= FDR-BH" 25significant genes after run t-test it told me that there is 25 5significant genes , all what i want to display these 25 genes by the way the structure of Result of test( rbasalt), also can i save this genes in excel file or text file > rbasalt[1:5,] probeID Stat RawpValue AdjpValue 1 AATK_E63_R 2.0216082 0.06002803 0.2962039 2 AATK_P519_R 0.7427987 0.46567086 0.6881159 3 AATK_P709_R 1.1541733 0.26102790 0.5323130 4 ABCA1_E120_R -2.5309415 0.01903356 0.1651541 5 ABCA1_P45_F -0.4280318 0.67279141 0.8117478 -- Best Regards, Islam Amin. [[alternative HTML version deleted]]

On 09/01/2012 04:00 AM, Islam Amin wrote: > i am using EMA package for mining gene expression data , i need to get list > of gene expression. > here is some of code: Hi -- EMA is a CRAN package so the correct person to ask is packageMaintainer("EMA")$Maintainer Martin > >> rbasalt <- runTtest(basalt, blabelt,typeFDR="FDR-BH",algo="t", q=0.01, > plot=TRUE) > Launch t test > Calculate pval > Adjusted pval > [1] "typeFDR= FDR-BH" > 25significant genes > > after run t-test it told me that there is 25 5significant genes , all what > i want to display these 25 genes by the way the structure of Result of test( > rbasalt), also can i save this genes in excel file or text file > > >> rbasalt[1:5,] > probeID Stat RawpValue AdjpValue > 1 AATK_E63_R 2.0216082 0.06002803 0.2962039 > 2 AATK_P519_R 0.7427987 0.46567086 0.6881159 > 3 AATK_P709_R 1.1541733 0.26102790 0.5323130 > 4 ABCA1_E120_R -2.5309415 0.01903356 0.1651541 > 5 ABCA1_P45_F -0.4280318 0.67279141 0.8117478 > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793