Question: Differential gene expression in edgeR
0
gravatar for n.naharfancy
6 months ago by
n.naharfancy0 wrote:

Hi,

I am a newbie in R and edgeR. I am calculating DEs in different samples. For example I have 6 paired samples of drug treatment. I want to test for DEs before and after. I found 110 DEs after drug administration. Now I want to see the logFC of those 110 genes in each individual to check if they all change in the same direction. How can I do that? I have used glm approach for paired samples. Thanks in advance.

rna-seq • 305 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by n.naharfancy0

On what basis you are saying 110 genes are deferentially expressed ? I think if you know the answer, you can filter the DE object based on fold change and significance level. pardon me If i am missing something.

ADD REPLYlink written 6 months ago by Prakash1.4k

It would only really be possible to do this if you rewrote your design with a different factor level for each of your 12 samples, and did a within-patient contrast for each patient. I suspect edgeR would complain due to the lack of degrees-of-freedom in the model, howver, I believe other people do use edgeR without replicates so it maybe possilbe.

I don't think it adds much to your analysis though, and will probably lead to you throwing out some really good candidates.

ADD REPLYlink written 6 months ago by russhh4.6k

thank you very much. No I just want to see if the fold change in the DE matches in each individual as I assume the fold change in the final DE list may be an average of all 6 individuals. Will you please explain the design matrix a little bit more?

ADD REPLYlink written 6 months ago by n.naharfancy0

Thank you very much for your reply. I have run the glm model from edgeR following the example given in the manual section 4.1. using patient and treatment as additive factors. Now I want to see the foldchange of those genes in each individual.

ADD REPLYlink written 6 months ago by n.naharfancy0

logFC of those 110 genes in each individual

You can't see logFC in each individual, because logFC are ratios - you need at least two individuals for the comparison. Maybe you want the counts for each gene for each individual? You can use edgeR function cpm().

ADD REPLYlink modified 6 months ago • written 6 months ago by h.mon27k

I think the logFC alluded to is drug vs no-drug in a given individual

ADD REPLYlink written 6 months ago by russhh4.6k

yes, that is what I want to check. Any suggestions how to do that?

ADD REPLYlink written 6 months ago by n.naharfancy0

logFC values in edgeR are not reliable, if you want to include FC anyway in your edgeR analysis, you'll have to use treat function. For detailed questions about why logFCs are not reliable in edgeR please ask them at bioconductor, since the authors of the package only answer the question there, not here at biostars.

ADD REPLYlink written 6 months ago by Benn7.4k
0
gravatar for n.naharfancy
6 months ago by
n.naharfancy0 wrote:

Well, there is this option in edgeR to calculate logFC when there is no replicates. Can I run that test on each individual samples assuming there is not replicates? But this model requires an estimation of BCV. Can I use the BCV calculated from all six sample analysed together to be used in this model. edgeR manual section 2.11

ADD COMMENTlink written 6 months ago by n.naharfancy0
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