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aldex2
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Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2
modelmatrix
covariates
2.4 years ago
amir
• 0
0
votes
3
replies
3.3k
views
How to correctly interpret ALDEx2 output - differential abundance testing
MicrobiomeData
ALDEx2
updated 2.7 years ago by
Lucie
• 0 • written 3.0 years ago by
RvH
• 0
0
votes
0
replies
1.0k
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
3.0 years ago
cwarden45
• 0
1
vote
4
replies
2.0k
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How to create an aldex.clr object from a "selex" data table
ALDEx2
3.5 years ago
Greg
• 0
0
votes
0
replies
974
views
Aldex2 BioCParallel issues
aldex2
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
jc235601
▴ 20
2
votes
0
replies
1.2k
views
Aldex2 error following tutorial - complex study design
software error
aldex2
6.5 years ago
mstagliamonte
▴ 10
0
votes
0
replies
1.3k
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
7.0 years ago
mstagliamonte
▴ 10
7 results • Page
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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…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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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