Question

how to export data as excel file from plotSmear when using edgeR

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linya • 0

@linya-11536

Last seen 8.4 years ago

Hi,

I am using edgeR to analyze differential expression of my RNA-Seq data. I am getting a plot of log-fold change vs log-counts per million with plotSmear function. I am wondering how can I export all the data as excel file containing gene name, logFC, logCPM, PValue, and FDR. Thanks!

edger • 1.3k views

ADD COMMENT • link updated 8.4 years ago by Gordon Smyth 52k • written 8.4 years ago by linya • 0

score 3 · Accepted Answer · 2016-09-22

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Gordon Smyth 52k

@gordon-smyth

Last seen 5 hours ago

WEHI, Melbourne, Australia

Have you done a DE analysis? What you are asking for is the toptags table produced by the topTags() function:

tab <- topTags(lrt)
write.csv(tab, file="myfile.csv")

ADD COMMENT • link 8.4 years ago Gordon Smyth 52k

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Thanks so much! Gordon. I just tried your code. It only shows the top 10 genes.

I would like to have all the up or downregulated gene list with logFC, logCPM, Pvalue, and FDR. Would you have some suggestions? Thanks!

ADD REPLY • link 8.4 years ago linya • 0

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If you read ?topTags, you can see that the n parameter is the relevant argument. Try setting n=Inf.

ADD REPLY • link 8.4 years ago Aaron Lun ★ 28k

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Thanks! It works!

> tab<-topTags(lrt,n=Inf)
> write.csv(tab,file="my file.csv")

ADD REPLY • link 8.4 years ago linya • 0