Question

Differential expression of individual genes using edgeR

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fawazfebin ▴ 60

@fawazfebin-14053

Last seen 4.7 years ago

Hi I would like to determine the differential expression of some of the selected genes from the plot I obtained in edgeR DE analysis. Are there any plots which we can construct which would depict the differential expression of a single gene between the samples ?

edger differential gene expression • 1.6k views

ADD COMMENT • link 7.5 years ago fawazfebin ▴ 60

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Sir , How do we get to know which of the genes are differentially expressed from the smear plot of DE in edgeR ? For example , I wanted to know if the gene ORAI1 has been up regulated or down regulated in the sample with respect to control : How will I interpret it from the smear plot of edgeR? I would like to know the steps involved. Kindly guide.

ADD REPLY • link 7.5 years ago fawazfebin ▴ 60

score 0 · Answer 1 · 2017-10-01

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Gordon Smyth 52k

@gordon-smyth

Last seen 6 hours ago

WEHI, Melbourne, Australia

Do you simply want to plot the individual expression values for a particular gene? Most people use cpm() or rpkm() to extract individual expression values from the DGEList object. Then you can use standard R plots to depict the values for any single gene.

As you will know from reading the documentation, you need to use topTags() or decideTests() to assess which genes are significantly differentially expressed. Obviously you can't just judge DE from a smearplot or MD plot, because those plots only show fold changes without showing variability.

ADD COMMENT • link 7.5 years ago Gordon Smyth 52k

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Yes i did want to plot the individual expression values.Thanks for your help Sir!

ADD REPLY • link 7.5 years ago fawazfebin ▴ 60