mkatari-bioinformatics-august-2013-clustering
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:48] – mkatari | mkatari-bioinformatics-august-2013-clustering [2015/06/17 13:26] (current) – mkatari | ||
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| ====== 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:// | ||
| + | [[https:// | ||
| + | |||
| + | In case you didn't get DESeq to work download and load the files above | ||
| + | |||
| + | < | ||
| + | resSig = read.table(" | ||
| + | normalized = read.table(" | ||
| + | |||
| + | </ | ||
| 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 | ||
| < | < | ||
| - | sigGenes.normalized = normalized[sigGenes, | + | sigGenes.normalized = normalized[as.character(sigGenes),] |
| </ | </ | ||
| Line 90: | Line 101: | ||
| < | < | ||
| - | SigGenes.kmeans.2 = kmeans(t(scaledSigGenes), 2, nstart=25) | + | SigGenes.kmeans.2 = kmeans(scaledSigGenes, |
| </ | </ | ||
| Line 168: | Line 179: | ||
| < | < | ||
| + | install.packages(" | ||
| library(gplots) | library(gplots) | ||
| </ | </ | ||
| Line 187: | Line 199: | ||
| < | < | ||
| pdf(" | 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.1418647726.txt.gz · Last modified: 2014/12/15 12:48 by mkatari