Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:17] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2015/08/21 13:53] – mkatari
@@ Line 21: / Line 21: @@
 First we will load the count data file.
 <code>
-counts = read.table(pathToCountsData, header=T, row.names=1)
+counts = read.table("NextGenRaw.txt", header=T, row.names=1)
 </code>
 Then we will load the experimental design. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOaE5fTVVhUHJKazg/edit?usp=sharing|here]]:
 <code>
-expdesign = read.table(pathToExpDesign)
+expdesign = read.table("expdesign.txt")
 </code>
@@ Line 53: / Line 53: @@
 An important part of DESeq is to estimate dispersion. This is simply a form of variance for the genes.
 <code>
+# if you have replicates do the following:
 cds = estimateDispersions( cds )
+### HOWEVER, If you have NO replicates, then try this
+cds = estimateDispersions( cds, method="blind" )
 </code>
@@ Line 85: / Line 88: @@
 #To get the genes that have FDR of 10% and save it in the output directory.
 <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",
             col.names=T,