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Virangika
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updated 6 months ago by
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
updated 14 months ago by
ATpoint
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written 14 months ago by
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updated 15 months ago by
Michael Love
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written 15 months ago by
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2.7 years ago
mb1996
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Comment: DESeq2 setting significant p-value
by
Michael Love
41k
```
> counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL))
> coldata <- data.frame(x=1:4)
> DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
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0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
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0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize
by
James W. MacDonald
65k
```
> library(AnnotationHub)
> hub <- AnnotationHub()
|===========================| 100%
snapshotDate(): 2023-10-23
> query(hu…
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