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Why DESeq2 gives large logfold for group with all zero count?
microbiome
16s
deseq2
differential gene expression
6.9 years ago
lanhuong
▴ 20
0
votes
5
replies
3.6k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
jbatsx
• 0
0
votes
2
replies
843
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2
16s
microbiome
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
mstagliamonte
▴ 10
0
votes
2
replies
806
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.1 years ago
vollkorrn
• 0
2
votes
1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
Katelyn
▴ 10
0
votes
1
reply
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.5 years ago
andrebolerbarros
▴ 20
0
votes
0
replies
902
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.4 years ago
mstagliamonte
▴ 10
7 results • Page
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Recent ...
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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