0
votes
0
replies
1.1k
views
onechannelGUI error,
probe oneChannelGUI probe oneChannelGUI
16.7 years ago PJARES@clinic.ub.es ▴ 30
0
votes
0
replies
2.7k
views
comparing affymetrix and agilent microarray data
cdf probe affy cdf probe affy
16.7 years ago Jarek Bryk ▴ 110
0
votes
1
reply
1.2k
views
autocorrelation analysis
updated 16.7 years ago by ▴ 50 • written 16.7 years ago by ▴ 200
0
votes
6
replies
2.7k
views
GEOquery and parsing SOFT files
GEOquery GEOquery
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 180
0
votes
4
replies
1.7k
views
xps - number of probesets for HuGene10ST array
Microarray Normalization xps Microarray Normalization xps
16.7 years ago Michael Walter ▴ 160
0
votes
1
reply
952
views
About NormExp+offset=50
updated 16.7 years ago by ▴ 400 • written 16.7 years ago by ▴ 380
2
votes
2
replies
3.8k
views
(control vs treatment) in (wildtype vs mutant) microarray analysis
affy limma affy limma
updated 16.7 years ago by ▴ 400 • written 16.7 years ago by ▴ 100
0
votes
0
replies
1.5k
views
Simple beadarraySNP analysis
SNP Normalization Cancer Colon PROcess beadarraySNP copynumber SNP Normalization Cancer
16.7 years ago Dmitri Mouradov ▴ 20
0
votes
0
replies
772
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Rmaanova with nested design: model construction
Microarray Microarray
16.7 years ago Aurélie Bonin ▴ 10
0
votes
3
replies
6.3k
views
upregulated or downregulated?
Cancer limma Cancer limma
updated 16.7 years ago by ▴ 400 • written 16.7 years ago by ▴ 20
0
votes
12
replies
2.6k
views
quantile robust and RMA in xps
Normalization PROcess xps Normalization PROcess xps
updated 16.7 years ago by ★ 3.9k • written 16.7 years ago by ▴ 510
0
votes
3
replies
1.7k
views
maSigPro and EMV no longer available for windows.
maSigPro maSigPro
updated 16.7 years ago by ▴ 340 • written 16.7 years ago by ▴ 540
0
votes
0
replies
786
views
Software Demo for Summer Research Grant
Network Network
16.7 years ago RICHARD SEGALL ▴ 10
0
votes
0
replies
629
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Microarray experimental designs
Microarray Microarray
16.7 years ago Usuario R ▴ 10
0
votes
3
replies
1.9k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 80
0
votes
0
replies
710
views
AnnotationDbi for organisms not on bioconductor.org
Annotation Annotation
16.7 years ago Michael Muratet ▴ 420
0
votes
2
replies
1.2k
views
no applicable method for "LD"
16.7 years ago Basu, Analabha ▴ 40
0
votes
2
replies
1.6k
views
Nimblegen / Ringo / Preprocess error: inherits(myRG, "RGList") is not TRUE
Preprocessing Homo sapiens probe Ringo Preprocessing Homo sapiens probe Ringo
16.7 years ago JEAN-YVES SGRO ▴ 20
0
votes
4
replies
1.9k
views
"GOstat" package not installing
GO GO
16.7 years ago Ashwin Kumar ▴ 90
0
votes
2
replies
1.2k
views
beadarray: outliers but not summary in log2-scale?
updated 16.7 years ago by ★ 1.1k • written 16.7 years ago by ▴ 830
0
votes
0
replies
938
views
intraSpotCorrelation
oligo oligo
16.7 years ago Gordon Smyth 53k
0
votes
2
replies
1.0k
views
Problem with duplicateCorrelation in LIMMA
limma limma
updated 16.7 years ago by 53k • written 16.7 years ago by ▴ 20
0
votes
3
replies
1.6k
views
problem with biocLite("Biobase") -- results in looping of download
Cancer Biobase Cancer Biobase
updated 16.7 years ago by ▴ 830 • written 16.7 years ago by 25k
0
votes
3
replies
1.9k
views
FlowViz graphics problems
flowCore flowViz flowCore flowViz
updated 16.7 years ago by ▴ 220 • written 16.7 years ago by ▴ 20
0
votes
1
reply
962
views
Basic Q on dye- swap
Microarray limma Microarray limma
updated 16.7 years ago by ▴ 400 • written 16.7 years ago by ▴ 60
0
votes
0
replies
1.3k
views
Important Message Notification
16.7 years ago Abbey National Plc ▴ 10
0
votes
1
reply
934
views
Category: testing for non-random chromosomal distribution of DE genes
GO Organism drosophila2 GO Organism drosophila2
updated 16.7 years ago by ★ 7.2k • written 16.7 years ago by ▴ 320
0
votes
2
replies
1.6k
views
Problem with Hopach: "Error in dmat[ord, ]"
drosophila2 hopach drosophila2 hopach
updated 16.7 years ago by 6.7k • written 16.7 years ago by ▴ 320
0
votes
1
reply
931
views
how to merge replicate spots
probe limma probe limma
updated 16.7 years ago by ★ 2.0k • written 16.7 years ago by ▴ 200
0
votes
0
replies
1.8k
views
LIMMA contrast matrix for three-way ANOVA with many comparisons
Cancer limma Cancer limma
16.7 years ago Levi Waldron ★ 1.1k
0
votes
0
replies
1.3k
views
problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
16.7 years ago Georg Otto ▴ 510
0
votes
2
replies
2.8k
views
PWM matching using matchPWM in Biostrings
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 16.7 years ago by ★ 1.6k • written 16.7 years ago by ▴ 10
0
votes
0
replies
1.2k
views
question about separating color channels for dual-channel cDNA microarray
Microarray Microarray
16.7 years ago Wei Xu ▴ 100
0
votes
2
replies
1.3k
views
limma and matrix design for single channel arrays - in search of a primer.
Microarray limma Agi4x44PreProcess Microarray limma Agi4x44PreProcess
updated 16.7 years ago by 68k • written 16.7 years ago by ▴ 390
0
votes
0
replies
1.8k
views
maSigPro time problem (2.trial)
maSigPro maSigPro
16.7 years ago Klaus-Peter Pleissner ▴ 70
0
votes
4
replies
1.4k
views
Affy output
Annotation GO hgu133a2 hgu133plus2 cdf Annotation GO hgu133a2 hgu133plus2 cdf
16.7 years ago Sarmah, Chintanu Kumar ▴ 70
0
votes
2
replies
1.2k
views
mislinked task views?
Cancer Category Cancer Category
updated 16.7 years ago by 6.7k • written 16.7 years ago by ▴ 180
0
votes
1
reply
1.9k
views
problems of GenABEL
SNP SNP
updated 16.7 years ago by 6.7k • written 16.7 years ago by ▴ 30
0
votes
3
replies
1.5k
views
RWebServices failing on mkserver (ant) target.
RWebServices RWebServices
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 60
0
votes
0
replies
1.2k
views
problem with biocLite("Biobase") -- results in looping of download
Biobase Biobase
16.7 years ago Mark W Kimpel ▴ 830
0
votes
0
replies
909
views
problem with reading agilent microarray data into agi4x44preprocess
mgug4122a Agi4x44PreProcess mgug4122a Agi4x44PreProcess
16.7 years ago Jarek Bryk ▴ 110
0
votes
4
replies
1.8k
views
Stange message with getOption("device") in OSX
updated 16.7 years ago by 6.7k • written 16.7 years ago by ▴ 50
0
votes
0
replies
1.1k
views
nsFilter() errors on ExpressionSetIllumina data object
Annotation Normalization GO Annotation Normalization GO
16.7 years ago Elliot Kleiman ▴ 150
0
votes
14
replies
2.6k
views
memory invalid permission with qc()
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 450
0
votes
5
replies
1.7k
views
Error from using featureFilter (genefilter package)
genefilter genefilter
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 80
0
votes
1
reply
1.1k
views
Further analysis after using MEDME?
probe probe
updated 16.7 years ago by ▴ 200 • written 16.7 years ago by ▴ 90
0
votes
1
reply
1.1k
views
past bioc releases
affy affy
updated 16.7 years ago by ▴ 150 • written 16.7 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Lumi: GenomStudio vs BeadStudio
GO lumi GO lumi
16.7 years ago Ingrid H. G. Østensen ▴ 700
0
votes
0
replies
735
views
On the house bets for an entire day
16.7 years ago Platinum Play ▴ 10
0
votes
0
replies
1.1k
views
Call for participants of CAMDA2009
Sequencing Sequencing
16.7 years ago Pan Du ★ 1.2k
46,725 results • Page 712 of 935
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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