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mkatari-bioinformatics-august-2013-deseq [2015/06/17 08:19] – mkatarimkatari-bioinformatics-august-2013-deseq [2015/06/17 09:06] – mkatari
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 Then we will load the experimental design. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOaE5fTVVhUHJKazg/edit?usp=sharing|here]]: Then we will load the experimental design. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOaE5fTVVhUHJKazg/edit?usp=sharing|here]]:
 <code> <code>
-expdesign = read.table(pathToExpDesign)+expdesign = read.table("expdesign.txt")
 </code> </code>
  
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 #To get the genes that have FDR of 10% and save it in the output directory. #To get the genes that have FDR of 10% and save it in the output directory.
 <code> <code>
-resSig = res[ which(res$padj < 0.1), ]+resSigind = res[ which(res$padj < 0.1 & res$log2FoldChange > 1), ] 
 +resSigrep = res[ which(res$padj < 0.1 & res$log2FoldChange < -1), ]
  
-outfile = "Deseq.results.txt" +indoutfile = "Deseq.indresults.txt"  
 +repoutfile = "Deseq.represults.txt" 
  
-write.table(resSig,  +write.table(resSigind,  
-            outfile, +            indoutfile,  
 +            sep="\t",  
 +            col.names=T,  
 +            row.names=F, 
 +            quote=F) 
 + 
 +write.table(resSigrep,  
 +            repoutfile, 
             sep="\t",              sep="\t", 
             col.names=T,              col.names=T, 
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari