User Tools

Site Tools



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

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:52]
mkatari-bioinformatics-august-2013-clustering [2015/06/17 13:26] (current)
Line 4: Line 4:
 ====== Clustering rna-seq data ====== ====== Clustering rna-seq data ======
 continuation from [[mkatari-bioinformatics-august-2013-deseq|DESeq]] continuation from [[mkatari-bioinformatics-august-2013-deseq|DESeq]]
 +In case you didn't get DESeq to work download and load the files above
 +resSig = read.table("resSig.txt", header=T)
 +normalized = read.table("normalized.txt", header=T, row.names=1)
 Get the significant genes Get the significant genes
Line 12: Line 23:
 Get the normalized values for the significant genes Get the normalized values for the significant genes
 <code> <code>
-sigGenes.normalized = normalized[sigGenes,]+sigGenes.normalized = normalized[as.character(sigGenes),]
 </code> </code>
Line 168: Line 179:
 <code> <code>
 library(gplots) library(gplots)
 </code> </code>
Line 187: Line 199:
 <code> <code>
 pdf("heatmap.pdf") pdf("heatmap.pdf")
-heatmap.2(sigGenes.normalized, +heatmap.2(as.matrix(sigGenes.normalized)
           col=redgreen(75),           col=redgreen(75),
           hclustfun=hclust2,           hclustfun=hclust2,
mkatari-bioinformatics-august-2013-clustering.1418647928.txt.gz · Last modified: 2014/12/15 12:52 by mkatari