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twochannel
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5
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Limma Design Matrix for two channel agilent arrays (direct experimental design)
Limma
limma design matrix
agilent
twochannel
7.0 years ago
pm2015
• 0
3
votes
9
replies
1.4k
views
Single channel analysis of two-color agilent array using limma
agilent
limma
twochannel
microarray
updated 7.4 years ago by
Gordon Smyth
47k • written 7.4 years ago by
pm2015
• 0
3
votes
8
replies
766
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma
microarray
design matrix
twochannel
updated 4.5 years ago by
Gordon Smyth
47k • written 4.5 years ago by
rubi
▴ 110
0
votes
4
replies
1.1k
views
snapCGH fails in runBioHMM
aCGH
Microarray
TwoChannel
Cancer
limma
aCGH
snapCGH
aCGH
Microarray
TwoChannel
Cancer
updated 13.7 years ago by
Wolfgang Raffelsberger
▴ 160 • written 13.7 years ago by
Ramon Diaz
★ 1.1k
1
vote
2
replies
1.8k
views
summarization for G4110B two colors agilent array: how to?
marray
agilent
twochannel
normalization
limma
updated 8.1 years ago by
Gordon Smyth
47k • written 8.1 years ago by
Andrea Grilli
▴ 240
0
votes
2
replies
3.0k
views
failure in GDS2eSet() in package GEOquery
Microarray
OneChannel
TwoChannel
DataImport
bridge
GEOquery
Microarray
OneChannel
bridge
updated 15.3 years ago by
Sean Davis
21k • written 15.3 years ago by
Wittner, Ben
▴ 290
3
votes
1
reply
2.5k
views
WGCNA: single channel microarray, one categorical covariate, how to apply it?
wgcna
twochannel
onechannel
updated 8.2 years ago by
Peter Langfelder
★ 2.7k • written 8.2 years ago by
jeiroje
▴ 20
0
votes
1
reply
837
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress
twochannel
microarray
5.3 years ago
Andy91
▴ 60
0
votes
1
reply
875
views
read.maimages problem under sun ?
Microarray
OneChannel
TwoChannel
DifferentialExpression
Preprocessing
QualityControl
affy
15.7 years ago
Amin Moghaddasi
▴ 130
9 results • Page
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Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
Michael Love
39k
Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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