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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
20 months ago
amir
• 0
0
votes
3
replies
2.7k
views
How to correctly interpret ALDEx2 output - differential abundance testing
MicrobiomeData
ALDEx2
updated 23 months ago by
Lucie
• 0 • written 2.2 years ago by
RvH
• 0
0
votes
0
replies
822
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
2.2 years ago
cwarden45
• 0
1
vote
4
replies
1.7k
views
How to create an aldex.clr object from a "selex" data table
ALDEx2
2.7 years ago
Greg
• 0
0
votes
0
replies
818
views
Aldex2 BioCParallel issues
aldex2
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
jc235601
▴ 20
2
votes
0
replies
1.1k
views
Aldex2 error following tutorial - complex study design
software error
aldex2
5.7 years ago
mstagliamonte
▴ 10
0
votes
0
replies
1.1k
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
6.2 years ago
mstagliamonte
▴ 10
7 results • Page
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Comment: Use of limma R package with targeted proteomics for DE analysis
by
svlachavas
▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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