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lfcshrink
•
reset
4
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4
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807
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DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago
bhandary.8590
▴ 20
3
votes
4
replies
862
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
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
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
0
votes
4
replies
674
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 4 months ago by
Igor
• 0
0
votes
2
replies
526
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
6 results • Page
1 of 1
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Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
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…
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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