Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
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@reubenmcgregor88-13722
Last seen 3.8 years ago

I have been handed a list of genes from an RNAseq experiment and I have no information about how it was generated as it was done a while ago by a company. I have the lis of genes in columns and pvalues/fold change for different comparisons. I also have the normalised expression values for each gene from each donor.

I have been asked to do some pathway analysis on this and was wondering about the best way to carry this out? I would rather not use arbitrary cut-offs of p-values etc but would rather do some kind of GSEA in R. 

It seems the limma package integrates analyses like camera for this, but am not sure I can simple use the data I have or which format they need to be to use within the limma package?

Any other advice about which packages to use?

 

 

rnaseq pathway analysis R limma • 1.6k views
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How long a list of genes do you have? Do you have just a short list of DE genes or do you have p-values and logFCs for a whole microarray (say)?

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I have a long list of about 20,000, from an array.

Thanks

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@lluis-revilla-sancho
Last seen 10 days ago
European Union

If you have the sample normalized expression you can load it to R and use camera or other tools in limma, or even other gene set enrichment analysis. However as you have the p-values (and I assume the t-values) you can use fgsea to make a GSEA like the one in Broad Institute webpage using the rank of your genes.

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