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DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis
meanSd
genefilter
DESeq2
20 months ago
Ndimensional
▴ 20
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Comment: Group-specific condition effects with individuals nested: matrix is not full ra
by
picasa1983
• 0
sorry I made a typo in my table (now edited). The donor 4 actually has the 2 conditions: KO and WT. I tried something, could it be the rea…
Comment: Group-specific condition effects with individuals nested: matrix is not full ra
by
ATpoint
★ 4.7k
The problem is that donor 4 is nested with condition since it is KO for both the donor 4 samples. Removing that and then making a new donor…
Comment: Group-specific condition effects with individuals nested: matrix is not full ra
by
James W. MacDonald
68k
What happens if you remove the columns of all zeros?
Comment: Error in retrieving clinical data
by
boidnoid
• 0
I was having the same problem. You can check the answer in a [previous post][1]. Specifically, reinstalling the devel version from GitHub …
Answer: How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differenti
by
James W. MacDonald
68k
The short answer is yes. When you compute pseudo-bulk estimates, the counts/gene are expected to be somewhat proportional to the number of …
Votes
Interpreting DESEQ2 interaction term and inclusion of covariate
A: Seurat/DESeq2 - single cell RNA-seq differential expression
Answer: Plot title for PCA in DESeq2
A: DESeq2: detect significantly increasing across an ordinal variable
Answer: DEseq2 design for additive treatment
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