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calebclass / NanoTube

Easy NanoString data analysis
GNU General Public License v3.0
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Request: option to keep control genes in 'runLimmaAnalysis' #1

Closed hendrikweisser closed 1 year ago

hendrikweisser commented 1 year ago

First, thanks for making this package available!

For some QC applications (e.g. MA plots) and comparisons to other methods, it can be useful to see what happens to the control genes (positive, negative, housekeeping) during differential expression analysis. Currently these genes are removed in runLimmaAnalysis: https://github.com/calebclass/NanoTube/blob/026563de287e07507f9ee6999d9fd25a9ac08663/R/runLimmaAnalysis.R#L51-L54

Would it be possible to add an option to runLimmaAnalysis to keep the control genes (and process them like the rest)?

calebclass commented 1 year ago

@hendrikweisser So sorry for the delay! I think I've resolved this. Please let me know if you have any trouble.