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confounding
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Use of confounders in downstream analysis
limma
GSA
confounding
within-pair analysis
450k
9.6 years ago
Aileen Bahl
▴ 10
1
vote
9
replies
3.9k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
9.1 years ago
Loodramon
• 0
8
votes
3
replies
3.0k
views
[Limma] Testing continuous variable with interaction
limma
voom
continuous
interactions
confounding
8.2 years ago
lanhuong
▴ 20
1
vote
6
replies
2.5k
views
adjusting for confounding effects in edgeR
edger
confounding
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Victoria
• 0
0
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0
replies
1.2k
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Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma
batch effect
design matrix
microarray
confounding
7.6 years ago
svlachavas
▴ 840
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Comment: lfcShrink and alpha value
by
cropero
• 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states
by
Philippine
• 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states
by
Guido Hooiveld
★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Adam
• 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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