Question: Gene Set Enrichment Analysis with RNA-seq data
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gravatar for deepak18
14 months ago by
deepak1810
deepak1810 wrote:

I have TCGA data for RNA expression for breast cancer samples (log2 normalised fpkm values) and I want to perform GSEA on it to look which gene sets are enriched in cancer samples vs normal samples. Which is the best platform to perform GSEA with RNA-seq software? Which will better, the software by Broad Institute (http://software.broadinstitute.org/gsea/index.jsp) or the R package fgsea (https://bioconductor.org/packages/release/bioc/html/fgsea.html)?

rna-seq next-gen R • 639 views
ADD COMMENTlink written 14 months ago by deepak1810

Define what you mean by 'better'. Without objective criteria, this ends up being a matter of personal preference.

ADD REPLYlink written 14 months ago by Jean-Karim Heriche23k

Actually I am facing problems with both. For analysis of RNA-seq data with the software we need to filter out low count measurements. What cut off should I put for this filter step and do I need to do some more pre-processing before I can go with the analysis?

ADD REPLYlink written 14 months ago by deepak1810

You should update your question title to attract more knowledgeable people. Usually filtering is already done by the software/code used to infer DE (e.g. DESeq2).

ADD REPLYlink written 14 months ago by Jean-Karim Heriche23k

Thank you for the comments. I was able to perform GSEA using the software successfully without any pre-processing.

ADD REPLYlink written 14 months ago by deepak1810

Pre-processing and quality control of the data is necessary because of many reasons. Your results might change if you do it.

ADD REPLYlink written 14 months ago by Mahdiar Sadeghi0
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