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twochannel
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Limma Design Matrix for two channel agilent arrays (direct experimental design)
Limma
limma design matrix
agilent
twochannel
8.2 years ago
pm2015
• 0
3
votes
8
replies
1.3k
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 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
rubi
▴ 110
3
votes
1
reply
2.9k
views
WGCNA: single channel microarray, one categorical covariate, how to apply it?
wgcna
twochannel
onechannel
updated 9.4 years ago by
Peter Langfelder
★ 3.0k • written 9.4 years ago by
jeiroje
▴ 20
3
votes
9
replies
1.9k
views
Single channel analysis of two-color agilent array using limma
agilent
limma
twochannel
microarray
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
pm2015
• 0
1
vote
2
replies
2.1k
views
summarization for G4110B two colors agilent array: how to?
marray
agilent
twochannel
normalization
limma
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
Andrea Grilli
▴ 240
0
votes
1
reply
1.3k
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress
twochannel
microarray
6.5 years ago
Andy91
▴ 60
0
votes
1
reply
1.2k
views
read.maimages problem under sun ?
Microarray
OneChannel
TwoChannel
DifferentialExpression
Preprocessing
QualityControl
affy
16.9 years ago
Amin Moghaddasi
▴ 130
0
votes
2
replies
3.5k
views
failure in GDS2eSet() in package GEOquery
Microarray
OneChannel
TwoChannel
DataImport
bridge
GEOquery
Microarray
OneChannel
bridge
updated 16.5 years ago by
Sean Davis
21k • written 16.5 years ago by
Wittner, Ben
▴ 290
0
votes
4
replies
1.4k
views
snapCGH fails in runBioHMM
aCGH
Microarray
TwoChannel
Cancer
limma
aCGH
snapCGH
aCGH
Microarray
TwoChannel
Cancer
updated 14.9 years ago by
Wolfgang Raffelsberger
▴ 160 • written 14.9 years ago by
Ramon Diaz
★ 1.1k
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Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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