Can I do differential analysis without phenodata?
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4 months ago
margarett • 0

I am doing RNAseq with GSE32038 data and I don't have phenodata file. How can I create the phonodata file or how can I do the differential analysis without it?

RNAseq ngs • 251 views
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By "phenodata", do you just mean sample metadata? If so, yes you would need that to do differential expression because otherwise you have no idea what features to compare. oh, and I'm guessing that GSE32038 refers to the GEO accession number? It's not clear from the question what you're trying to do with it or why.

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Entering edit mode
4 months ago
ATpoint 60k

This seems to be a simple 2-group comparison. The info is in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32038

Samples (6)
GSM794483   Simulated Condition 1, replicate 1
GSM794484   Simulated Condition 1, replicate 2
GSM794485   Simulated Condition 1, replicate 3
GSM794486   Simulated Condition 2, replicate 1
GSM794487   Simulated Condition 2, replicate 2
GSM794488   Simulated Condition 2, replicate 3


So make a data.frame with a column group being the conditon and use ~group, that's it.