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log2FC
•
reset
1
vote
10
replies
5.9k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2
differential gene expression
log2fc
8.1 years ago
Osvaldo
▴ 40
6
votes
8
replies
5.7k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 17 months ago by
James W. MacDonald
65k • written 8.1 years ago by
serpalma.v
▴ 60
1
vote
3
replies
5.2k
views
log2 fold change calculation for DE gene analysis
deseq2
L2FC
log2fc
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
sup230
▴ 30
0
votes
4
replies
4.3k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2
log2FC
19 months ago
User000
• 0
0
votes
2
replies
3.8k
views
DESEq2 log2FoldChange and lfcSE calculations
deseq2
log2fc
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
David R
▴ 90
1
vote
5
replies
2.4k
views
log2FC calculation in EdgeR
edger
log2FC
written 4.5 years ago by
matteo.buti
• 0
1
vote
3
replies
2.3k
views
Log2 foldchange in DESeq2
deseq2
R
log2fc
updated 8.4 years ago by
Michael Love
41k • written 8.4 years ago by
Sushant Pawar
• 0
2
votes
2
replies
1.9k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2
chipseq
counts
log2fc
error
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
robin.uchiyama
• 0
1
vote
5
replies
1.8k
views
Log2FC values very small with SCAN
scan
Log2FC
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Vani
▴ 20
0
votes
3
replies
1.4k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2
log2fc
shrinkage
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
aec
▴ 90
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
2
votes
4
replies
1.3k
views
Standard error of log2FC from DESeq in time series experiment
deseq2
log2fc
standard error
timecourse
updated 6.2 years ago by
ellascottgm
• 0 • written 6.2 years ago by
Verena
• 0
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
16 months ago
Iwan
• 0
0
votes
1
reply
683
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2
LRT
multifactorial
up/down-reg
log2FC
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Laia
▴ 10
0
votes
2
replies
634
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
12 months ago
paria.alipour
• 0
15 results • Page
1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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