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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
8 months ago
amir
• 0
0
votes
3
replies
1.5k
views
How to correctly interpret ALDEx2 output - differential abundance testing
MicrobiomeData
ALDEx2
updated 11 months ago by
Lucie
• 0 • written 15 months ago by
RvH
• 0
0
votes
0
replies
488
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
15 months ago
cwarden45
• 0
1
vote
4
replies
1.2k
views
How to create an aldex.clr object from a "selex" data table
ALDEx2
21 months ago
Greg
• 0
0
votes
0
replies
625
views
Aldex2 BioCParallel issues
aldex2
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
jc235601
▴ 20
2
votes
0
replies
819
views
Aldex2 error following tutorial - complex study design
software error
aldex2
4.8 years ago
mstagliamonte
▴ 10
0
votes
0
replies
870
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.3 years ago
mstagliamonte
▴ 10
7 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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