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Showing :
ihw
•
reset
2
votes
4
replies
1.8k
views
Filtering after DESeq
DESeq2
IHW
written 7 months ago by
caroline.zanchi
▴ 10
0
votes
3
replies
1.3k
views
IHW for multiple regression
IHW
updated 2.9 years ago by
Wolfgang Huber
★ 13k • written 3.0 years ago by
Tyson
• 0
1
vote
3
replies
1.4k
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW
lfcShrink
DESeq2
3.6 years ago
Ali Barry
▴ 40
3
votes
2
replies
1.8k
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
4.0 years ago • updated 3.9 years ago
Bex
• 0
3
votes
3
replies
1.4k
views
IHW: retain annotation columns in data when running `ihw(pvalue ~ covariate, data = ...)`
ihw
independent hypothesis weighting
5.6 years ago
david.laehnemann
▴ 10
2
votes
4
replies
1.6k
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
rihards.saksis
• 0
0
votes
2
replies
1.2k
views
DESeq2 and data.table impacted by IHW and lpsymphony
lpsymphony
IHW
updated 6.1 years ago by
Mike Smith
★ 6.6k • written 6.1 years ago by
mattjdowle
• 0
1
vote
2
replies
1.4k
views
Does DESeq2 need to correct for overlapping regions?
deseq2
ihw
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
schwarzl
• 0
1
vote
2
replies
1.5k
views
IHW scale of problem
ihw
p-value
multiple hypothesis
updated 6.5 years ago by
Wolfgang Huber
★ 13k • written 6.5 years ago by
xiaotong.yao23
▴ 10
2
votes
3
replies
1.6k
views
lpsymphony will not build
ihw
6.6 years ago
caldodge
▴ 20
0
votes
2
replies
1.1k
views
Adjusting DESeq2 p-values through IHW using pathway information as covariate
IHW
deseq2
Pathway
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
guidobarzaghi
▴ 20
5
votes
6
replies
2.2k
views
DESeq2 w. pathway/network info as a prior knowledge
deseq2
pathway
ihw
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
guidobarzaghi
▴ 20
8
votes
2
replies
1.4k
views
Does IHW use the supplied alpha for the correction calculations?
IHW
deseq2
updated 6.8 years ago by
Nikos Ignatiadis
▴ 180 • written 6.8 years ago by
k.vitting.seerup
▴ 120
1
vote
4
replies
1.9k
views
IHW multiple testing correction
IHW
multiple testing correction
covariate distribution
updated 7.1 years ago by
Wolfgang Huber
★ 13k • written 7.1 years ago by
lara.h.urban
• 0
1
vote
3
replies
1.9k
views
IHW and correlated covariates
ihw
9.0 years ago • updated 4.5 years ago
Michael Love
43k
0
votes
6
replies
2.2k
views
Defining subsets for FDR correction
fdr
deseq2
ihw
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
sven.schenk
▴ 30
1
vote
3
replies
1.9k
views
Libgomp error in IHW
ihw
updated 7.7 years ago by
vladislav.kim
▴ 10 • written 7.8 years ago by
Kipper Fletez-Brant
▴ 150
2
votes
2
replies
1.9k
views
how to specify the number of cores used by IHW
IHW
lpsymphony
updated 8.2 years ago by
vladislav.kim
▴ 10 • written 8.2 years ago by
Charlotte Soneson
▴ 170
5
votes
1
reply
1.8k
views
IHWpaper: choice of `nbins=4` in `proteomics_example_analysis.R`
ihw
updated 8.5 years ago by
Nikos Ignatiadis
▴ 180 • written 8.5 years ago by
paul.johnston
▴ 10
1
vote
4
replies
2.2k
views
IHW Package for R 3.2.5
deseq2
ihw
8.6 years ago
bekah
▴ 40
1
vote
2
replies
2.5k
views
How to use 'IHW' package to filter genes?
ihw
deseq2
edger
limma voom
updated 8.9 years ago by
Bernd Klaus
▴ 610 • written 8.9 years ago by
tofukaj
• 0
10
votes
2
replies
1.7k
views
Possible to incorporate the sign or direction of an effect in the IHW covariate?
IHW
updated 9.7 years ago by
Nikos Ignatiadis
▴ 180 • written 9.7 years ago by
dhibar
▴ 60
22 results • Page
1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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