Showing : PEER • reset
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.2 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
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Comment: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by ATpoint ★ 4.8k
What is lac cells? You mean 7000-9000 cells? Please check first that the function runs OOM even without any of these multicore options set.…
Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Votes
Comment: Heatmap of rnaseq data with z-score scale
Answer: parameters of filterByExpr
Comment: Heatmap of rnaseq data with z-score scale
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
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