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Question: Differential expression of individual genes using edgeR
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gravatar for fawazfebin
7 weeks ago by
fawazfebin0
fawazfebin0 wrote:
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 ?
ADD COMMENTlink modified 6 weeks ago • written 7 weeks ago by fawazfebin0
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 REPLYlink written 6 weeks ago by fawazfebin0
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gravatar for Gordon Smyth
6 weeks ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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 COMMENTlink modified 6 weeks ago • written 6 weeks ago by Gordon Smyth32k
Yes i did want to plot the individual expression values.Thanks for your help Sir!
ADD REPLYlink written 6 weeks ago by fawazfebin0
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