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lfcshrink
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4
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674
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 4 months ago by
Igor
• 0
0
votes
2
replies
525
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
delphine.rossille
• 0
3
votes
4
replies
862
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
bhandary.8590
▴ 20
4
votes
4
replies
807
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Alina
• 0
6 results • Page
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Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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