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lfcshrink
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink
DESeq2
written 3 months ago by
Igor
• 0
0
votes
2
replies
491
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
delphine.rossille
• 0
3
votes
4
replies
838
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 8 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
bhandary.8590
▴ 20
4
votes
4
replies
784
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
10 months ago • updated 9 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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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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