mkatari-bioinformatics-august-2013-clustering
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mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:45] – 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 | ||
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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),] |
</ | </ | ||
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< | < | ||
- | SigGenes.kmeans.2 = kmeans(t(scaledSigGenes), 2, nstart=25) | + | SigGenes.kmeans.2 = kmeans(scaledSigGenes, |
</ | </ | ||
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for (i in 2:20) { | for (i in 2:20) { | ||
| | ||
- | | + | #alternate way of looking at proportion of ss that is provided by between groups. |
- | + | #kmeans_ss[i] = kmeans_tmp$betweenss/ | |
+ | |||
+ | # | ||
+ | | ||
+ | | ||
+ | |||
} | } | ||
return(kmeans_ss) | return(kmeans_ss) | ||
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</ | </ | ||
- | |||
- | </ | ||
The code below plots k-means clustering results. You simply have to provide the k-means output and the labels. | The code below plots k-means clustering results. You simply have to provide the k-means output and the labels. | ||
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< | < | ||
+ | install.packages(" | ||
library(gplots) | library(gplots) | ||
</ | </ | ||
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< | < | ||
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.txt · Last modified: 2015/06/17 13:26 by mkatari