Differences

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--- mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:15] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:17] – mkatari
@@ Line 58: / Line 58: @@
 To visualize the disperson graph
 <code>
-dispersionFile = paste(pathToOutputDir, "Dispersion.pdf", sep="")
+dispersionFile = "Dispersion.pdf"
 pdf(dispersionFile)
 plotDispEsts( cds )
@@ Line 77: / Line 77: @@
 <code>
-maFile = paste(pathToOutputDir, "MAplot.pdf", sep="")
+maFile = "MAplot.pdf"
 pdf(maFile)
 plotMA(res)
@@ Line 87: / Line 87: @@
 resSig = res[ which(res$padj < 0.1), ]
-outfile = paste(pathToOutputDir,"Deseq.results.txt", sep="")
+outfile = "Deseq.results.txt"
 write.table(resSig,