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mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:52]
mkatari
mkatari-bioinformatics-august-2013-clustering [2015/06/17 13:26] (current)
mkatari
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]]
 +
 +[[https://drive.google.com/file/d/0B172nc4dAaaORnh3MkZqUE9PVjA/view?usp=sharing|resSig.txt]]
 +[[https://drive.google.com/file/d/0B172nc4dAaaONXFIX2YxeDRCbkE/view?usp=sharing|normalized.txt]]
 +
 +In case you didn't get DESeq to work download and load the files above
 +
 +<code>
 +resSig = read.table("resSig.txt", header=T)
 +normalized = read.table("normalized.txt", header=T, row.names=1)
 +
 +</code>
  
 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>
 +install.packages("gplots")
 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