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arrayweights
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16
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3.7k
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simultaneous use of robust and weighting methods in limma
limma
robust
arrayWeights
10.4 years ago • updated 7.9 years ago
Gordon Smyth
50k
7
votes
2
replies
2.2k
views
Appropriate explanation of the methodology behind arrayWeights function from limma R package
limma
arrayWeights
variance
sampleQuality
microarray
updated 8.5 years ago by
Ryan C. Thompson
★ 7.9k • written 8.5 years ago by
svlachavas
▴ 830
10
votes
4
replies
2.1k
views
limma-trend with random effects and/or array weights
limma-trend
duplicatecorrelation
arrayweights
limma
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
maltethodberg
▴ 170
4
votes
8
replies
1.7k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma
duplicatecorrelation
arrayweights
microarray
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
svlachavas
▴ 830
4
votes
5
replies
1.6k
views
limma: genas + arrayweights = OK?
limma
genas
arrayweights
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
Guido Hooiveld
★ 3.9k
2
votes
2
replies
1.4k
views
Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma
duplicatecorrelation
arrayweights
8.5 years ago
willj
▴ 30
1
vote
2
replies
1.3k
views
limma normalization and arrayWeights fold change
limma
arrayweights
logfoldchange
neqc
normalization
updated 7.9 years ago by
svlachavas
▴ 830 • written 7.9 years ago by
merella.stefania
• 0
4
votes
1
reply
1.3k
views
simultaneous use of robust and weighting methods in limma.
limma
arrayweights
robust
updated 9.4 years ago by
Gordon Smyth
50k • written 10.4 years ago by
Richard Friedman
▴ 80
0
votes
1
reply
1.3k
views
Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma
microarray
multifactorial design
duplicatecorrelation
arrayweights
8.3 years ago
svlachavas
▴ 830
0
votes
1
reply
836
views
Illumina array weights--arrayWeights or beadCountWeights
limma
arrayweights
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
johnmcma
▴ 10
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Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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