Bioconductor SparseMatrix

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HiTC importC sparseMatrix

2.6 years ago shikha • 0

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Comment: Mean variance curve troubleshoot filtering by gingergeiger22 • 0

Gordon, thank for your response. 'filterByExpr()' was marginally better. I can see high variability in samples within the groups from the M…

Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data by rohitsatyam102 ▴ 20

Since I don't know which organism you are working on, I would recommend using the following: `-s 0` if library is unstranded `-C` Discard…

Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data by rohitsatyam102 ▴ 20

Yes use this option. It is recommended for PE and if you don't use it you will observe nearly twice the number of counts in your results. H…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper : ```` DGE_list_object <- estimateGLMR…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …

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Comment: Comparing different method for DESEQ2

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