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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k

Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…

Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k

Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…

Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…

Comment: Error in creating BSGenome package by Nguyen • 0

I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…

Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k

There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…

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C: ControlGenes/ housekeeping genes Deseq2

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