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ihw
•
reset
2
votes
4
replies
1.7k
views
Filtering after DESeq
DESeq2
IHW
written 6 months ago by
caroline.zanchi
▴ 10
0
votes
3
replies
1.2k
views
IHW for multiple regression
IHW
updated 2.7 years ago by
Wolfgang Huber
★ 13k • written 2.9 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
3.5 years ago
Ali Barry
▴ 40
3
votes
2
replies
1.7k
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
3.8 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
5.5 years ago
david.laehnemann
▴ 10
2
votes
4
replies
1.6k
views
DESeq2 - problem with inferring correct results.
deseq2
rnaseq
sva
fdrtool
ihw
updated 5.7 years ago by
Michael Love
43k • written 5.7 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 6.0 years ago by
Mike Smith
★ 6.6k • written 6.0 years ago by
mattjdowle
• 0
1
vote
2
replies
1.3k
views
Does DESeq2 need to correct for overlapping regions?
deseq2
ihw
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
schwarzl
• 0
1
vote
2
replies
1.4k
views
IHW scale of problem
ihw
p-value
multiple hypothesis
updated 6.4 years ago by
Wolfgang Huber
★ 13k • written 6.4 years ago by
xiaotong.yao23
▴ 10
2
votes
3
replies
1.6k
views
lpsymphony will not build
ihw
6.5 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 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
guidobarzaghi
▴ 20
5
votes
6
replies
2.1k
views
DESeq2 w. pathway/network info as a prior knowledge
deseq2
pathway
ihw
updated 6.7 years ago by
Michael Love
43k • written 6.7 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 6.7 years ago by
Nikos Ignatiadis
▴ 180 • written 6.7 years ago by
k.vitting.seerup
▴ 120
1
vote
4
replies
1.8k
views
IHW multiple testing correction
IHW
multiple testing correction
covariate distribution
updated 6.9 years ago by
Wolfgang Huber
★ 13k • written 6.9 years ago by
lara.h.urban
• 0
1
vote
3
replies
1.9k
views
IHW and correlated covariates
ihw
8.9 years ago • updated 4.3 years ago
Michael Love
43k
0
votes
6
replies
2.1k
views
Defining subsets for FDR correction
fdr
deseq2
ihw
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
sven.schenk
▴ 30
1
vote
3
replies
1.9k
views
Libgomp error in IHW
ihw
updated 7.6 years ago by
vladislav.kim
▴ 10 • written 7.6 years ago by
Kipper Fletez-Brant
▴ 150
2
votes
2
replies
1.8k
views
how to specify the number of cores used by IHW
IHW
lpsymphony
updated 8.1 years ago by
vladislav.kim
▴ 10 • written 8.1 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 8.4 years ago by
Nikos Ignatiadis
▴ 180 • written 8.4 years ago by
paul.johnston
▴ 10
1
vote
4
replies
2.1k
views
IHW Package for R 3.2.5
deseq2
ihw
8.5 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 8.7 years ago by
Bernd Klaus
▴ 610 • written 8.7 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 9.5 years ago by
Nikos Ignatiadis
▴ 180 • written 9.5 years ago by
dhibar
▴ 60
22 results • Page
1 of 1
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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