Question: How to extract genes with greatest BCV?
0
gravatar for Mich
15 months ago by
Mich0
Singapore
Mich0 wrote:

Hi,

I am analyzing RNAseq data using the EdgeR package and have made the MDS plot using the following code.

y<-DGEList(counts=data, group=Source)

keep<- rowSums(cpm(y)>1) >= 1

y<- y[keep, , keep.lib.sizes=FALSE]

y<-calcNormFactors(y)

plotMDS(y, method="bcv",dim= c(1,2), top=1000)

I am wondering if it is possible to obtain the gene names of the top 1000 genes with the greatest biological coefficient of variation.

Many thanks! 

edger • 252 views
ADD COMMENTlink modified 15 months ago by Aaron Lun25k • written 15 months ago by Mich0
Answer: How to extract genes with greatest BCV?
1
gravatar for Aaron Lun
15 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

The BCV is just the square root of the tagwise dispersion, so just take the top 1000 genes with the largest tagwise dispersions:

order(y$tagwise.dispersion, decreasing=TRUE)[1:1000]

... after you've run estimateDisp.

ADD COMMENTlink written 15 months ago by Aaron Lun25k

Thanks Aaron!

ADD REPLYlink written 15 months ago by Mich0
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