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Answer: Deseq2 sfType
by
James W. MacDonald
67k
This is a bit tricky. If you look at the help page for `DESeq`, it says ``` sfType: either "ratio", "poscounts", or "iterate" for the ty…
Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
by
Jane_Huang
• 0
I used scan 30 as an example: ```r >test2<-as.data.frame(id_filtered) >test3<-filter(test2,spectrumID="scan=30") >test3 sequence spec…
Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
by
Jane_Huang
• 0
Thank you very much for the detailed explanation!! Sorry for the delay response. Indeed, there were multiple MS2 scan matching to more than…
Comment: Normalization RNA-seq for multiple plates
by
ATpoint
★ 4.4k
What are "plates"? You mean sequencing runs? Have the libraries been prepared the same time or in a balanced / batch-aware fashion? Add som…
Comment: filterbyexp() in edgeR
by
Yunshun Chen
▴ 870
Since you only have 1 sample in `DonorD_01`, your `Gene_X` will not be filtered if it exceeds the CPM cut-off in at least 1 sample. In a ty…
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Answer: Deseq2 sfType
Answer: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
Answer: SAS token for Annotation package
Answer: SAS token for Annotation package
A: How featureCounts define the gene length
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