Question: Find details of co-variate which has effect on gene expression level using edgeR and DESeq2
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3.0 years ago by
star190
Netherlands
star190 wrote:

I have RNAseq data of patient and control samples with different age and gender. I would like to know whether these co-variate affect gene expression levels. If they do not have any effect remove them from model and create simpler model for differential expression analysis using edgeR and DESeq2. Would you please let me know if there is a function in these packages to find the answer? Actually, I would like to see details of models in edgeR and DESeq2 and then find which co-varate affect gene expression and which one do not have affect?

ADD COMMENTlink written 3.0 years ago by star190

Coincidentally a colleague told me today about http://bioconductor.org/packages/release/bioc/html/pcaExplorer.html, which would allow you to analyze (the effect of) covariates on your data. I haven't tested it, but perhaps it's something worth trying for your question.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by WouterDeCoster41k
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