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affyPLM
•
reset
0
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8
replies
1.8k
views
Biological replication (was RNA degradation problem)
Normalization
probe
affy
affyPLM
Normalization
probe
affy
affyPLM
18.2 years ago
Naomi Altman
★ 6.0k
0
votes
10
replies
1.6k
views
exonmap RMA function
Microarray
Cancer
affyPLM
exonmap
Microarray
Cancer
affyPLM
exonmap
updated 16.2 years ago by
Yuan Jian
▴ 250 • written 16.2 years ago by
Martin Morgan
25k
0
votes
5
replies
1.8k
views
affyPLM - cant plot chip pseudo image
cdf
genefilter
affy
affydata
affyPLM
simpleaffy
affyio
cdf
genefilter
affy
affydata
updated 16.7 years ago by
James W. MacDonald
65k • written 16.7 years ago by
Tagett Rebecca
▴ 50
0
votes
11
replies
2.6k
views
trouble hacking plotPCA
GO
Survival
Biobase
genefilter
affy
affydata
graph
limma
gcrma
matchprobes
affyPLM
RBGL
updated 17.3 years ago by
Rustici, Gabriella NIH/NCI [F]
▴ 10 • written 17.3 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.4k
views
objects masked from packages
affyPLM
affyPLM
updated 14.1 years ago by
James W. MacDonald
65k • written 14.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.1k
views
AffyPLM
affyPLM
affyPLM
updated 20.1 years ago by
Matthew Hannah
▴ 940 • written 20.1 years ago by
Yen Lin Chia
▴ 50
0
votes
2
replies
1.1k
views
Re: how to evaluate the arrays quality?
GO
affy
affyPLM
GO
affy
affyPLM
updated 18.8 years ago by
David Kipling
▴ 110 • written 18.8 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
2
replies
1.3k
views
gregmisc package-problems with BioC latest release?
Biobase
annotate
edd
genefilter
geneplotter
ROC
limma
siggenes
affyPLM
marray
Biobase
updated 19.4 years ago by
Seth Falcon
★ 7.4k • written 19.4 years ago by
Fátima Núñez
▴ 130
0
votes
3
replies
1.5k
views
identical output plots for NUSE AND RLE
GO
Cancer
affyPLM
GO
Cancer
affyPLM
updated 13.8 years ago by
Paolo Innocenti
▴ 320 • written 13.8 years ago by
Richard Friedman
★ 2.0k
0
votes
4
replies
1.7k
views
arrayQualityMetrics package - bugs and errors
limma
affyPLM
arrayQualityMetrics
limma
affyPLM
arrayQualityMetrics
updated 12.1 years ago by
Wolfgang Huber
★ 13k • written 12.1 years ago by
Vladimir Krasikov
▴ 90
0
votes
2
replies
1.6k
views
"AveExp" column has dissappeared from limma topTable
GO
Survival
annotate
geneplotter
affydata
limma
annaffy
affyPLM
GO
Survival
annotate
updated 17.0 years ago by
Gordon Smyth
50k • written 17.0 years ago by
Marcus Davy
▴ 680
0
votes
3
replies
1.1k
views
Images from exon arrays
affy
affyPLM
affy
affyPLM
13.5 years ago
Popovic, Jelena
▴ 20
0
votes
4
replies
1.4k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation
cdf
probe
affy
affyPLM
Annotation
cdf
probe
affy
affyPLM
updated 15.3 years ago by
James W. MacDonald
65k • written 15.3 years ago by
Peter White
▴ 130
0
votes
2
replies
856
views
loading affyPLM with R 2.4.
affyPLM
affyPLM
updated 17.6 years ago by
Ben Bolstad
★ 1.2k • written 17.6 years ago by
Oliver Hartmann
▴ 20
0
votes
3
replies
1.1k
views
Install of 1.5 Packages fails
GO
edd
genefilter
annaffy
affyPLM
marray
GO
edd
genefilter
annaffy
affyPLM
marray
updated 19.4 years ago by
rgentleman
★ 5.5k • written 19.4 years ago by
Thomas Girke
★ 1.7k
0
votes
3
replies
886
views
Error messages in affylmGUI on PC with respect to plotting
limma
affyPLM
affylmGUI
limma
affyPLM
affylmGUI
18.7 years ago
Seth Falcon
★ 7.4k
0
votes
2
replies
934
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf
gcrma
matchprobes
affyPLM
affyio
cdf
gcrma
matchprobes
affyPLM
affyio
updated 17.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.5 years ago by
k. brand
▴ 420
0
votes
4
replies
1.1k
views
MA plots for large number of arrays
affy
affyPLM
beadarray
lumi
affy
affyPLM
beadarray
lumi
updated 12.4 years ago by
boczniak767
▴ 720 • written 12.4 years ago by
Juliet Hannah
▴ 360
0
votes
2
replies
2.8k
views
Error in function (classes, fdef, mtable)
cdf
genefilter
reposTools
gcrma
matchprobes
affyPLM
simpleaffy
affyio
cdf
genefilter
updated 17.4 years ago by
Seth Falcon
★ 7.4k • written 17.4 years ago by
D.Enrique ESCOBAR ESPINOZA
▴ 360
0
votes
12
replies
1.9k
views
Some Genefilter questions
GO
Survival
cdf
genefilter
geneplotter
tkWidgets
affy
affydata
widgetTools
gcrma
affyPLM
updated 17.3 years ago by
rgentleman
★ 5.5k • written 17.3 years ago by
Amy Mikhail
▴ 460
0
votes
9
replies
1.8k
views
problem with duplicateCorrelation and ExpressionSet objects
GO
Survival
cdf
Biobase
graph
limma
gcrma
annaffy
affyPLM
simpleaffy
biomaRt
Category
updated 16.9 years ago by
Seth Falcon
★ 7.4k • written 16.9 years ago by
Jenny Drnevich
★ 2.2k
0
votes
5
replies
1.0k
views
how to rank affy probesets by their probe-effect magnitude
probe
affy
affyPLM
probe
affy
affyPLM
updated 12.1 years ago by
James W. MacDonald
65k • written 12.1 years ago by
Robert Castelo
★ 3.1k
0
votes
3
replies
1.2k
views
LIMMA No residual using rmaPLM
Preprocessing
affyPLM
Preprocessing
affyPLM
updated 18.6 years ago by
Gordon Smyth
50k • written 18.6 years ago by
Ron Ophir
▴ 270
0
votes
4
replies
1.7k
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 16.9 years ago by
Ben Bolstad
★ 1.2k • written 16.9 years ago by
Allen Day
▴ 30
0
votes
2
replies
1.1k
views
median of the NUSE value
cdf
affy
gcrma
affyPLM
affyio
cdf
affy
gcrma
affyPLM
affyio
updated 17.8 years ago by
Ben Bolstad
★ 1.2k • written 17.8 years ago by
kfbargad@ehu.es
▴ 270
0
votes
1
reply
1.2k
views
[R] problem loading affycoretools - solved!
Biobase
Ruuid
genefilter
multtest
graph
limma
gcrma
matchprobes
affyPLM
RBGL
simpleaffy
updated 17.6 years ago by
Seth Falcon
★ 7.4k • written 17.6 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
867
views
qc
Survival
Biobase
genefilter
affy
affydata
affyPLM
simpleaffy
affyio
Survival
Biobase
updated 17.6 years ago by
James W. MacDonald
65k • written 17.6 years ago by
Per.Broberg@astrazeneca.com
▴ 10
0
votes
2
replies
1.1k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization
affydata
gcrma
matchprobes
affyPLM
affyio
Normalization
affydata
gcrma
updated 17.5 years ago by
Ben Bolstad
★ 1.2k • written 17.5 years ago by
k. brand
▴ 420
0
votes
3
replies
2.0k
views
arrayQualityMetrics error on windows
affyPLM
affyPLM
11.6 years ago
Marcus Davy
▴ 390
0
votes
4
replies
1.4k
views
Problems with the size of the plots obtained with AffyPLM
cdf
affy
gcrma
affyPLM
affyio
cdf
affy
gcrma
affyPLM
affyio
updated 17.2 years ago by
Oosting, J. PATH
▴ 550 • written 17.2 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
1
reply
1.1k
views
Problems with packages: annaffy, GO, KEGG, golubEsets
GO
edd
annaffy
affyPLM
GO
edd
annaffy
affyPLM
updated 19.3 years ago by
rgentleman
★ 5.5k • written 19.3 years ago by
Vitalina Komashko
▴ 10
0
votes
6
replies
1.1k
views
What wrong with my data using LIMMA
Microarray
affy
limma
affyPLM
Microarray
affy
limma
affyPLM
updated 18.6 years ago by
Adaikalavan Ramasamy
★ 1.8k • written 18.6 years ago by
Gordon Smyth
50k
0
votes
1
reply
951
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 16.5 years ago by
Ben Bolstad
★ 1.2k • written 16.5 years ago by
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
1.4k
views
Bioconductor 1.4 released
Proteomics
Annotation
Normalization
GO
Cancer
CGH
pamr
gcrma
gpls
affyPLM
webbioc
bim
updated 19.9 years ago by
Wolfgang Huber
★ 13k • written 19.9 years ago by
A.J. Rossini
▴ 810
0
votes
1
reply
1.1k
views
affy package in MacOSX
affy
affydata
matchprobes
affyPLM
affy
affydata
matchprobes
affyPLM
updated 19.7 years ago by
James Wettenhall
▴ 1000 • written 19.7 years ago by
Tiago R Magalhaes
▴ 60
0
votes
5
replies
2.3k
views
error in ls() unused arguments
mouse4302
affyPLM
mouse4302
affyPLM
updated 15.1 years ago by
Laurent Gautier
★ 2.3k • written 15.1 years ago by
Wijchers, Patrick
▴ 40
0
votes
1
reply
1.0k
views
RNA degradation problem
Normalization
affy
limma
affyPLM
PROcess
Normalization
affy
limma
affyPLM
PROcess
updated 18.2 years ago by
Fangxin Hong
▴ 810 • written 18.2 years ago by
Matthew Hannah
▴ 940
0
votes
2
replies
1.1k
views
ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM
arrayQualityMetrics
affyPLM
arrayQualityMetrics
updated 14.4 years ago by
audrey
▴ 280 • written 14.4 years ago by
lohith madireddy
▴ 40
0
votes
2
replies
1.3k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray
Annotation
Normalization
Preprocessing
cdf
probe
affy
affyPLM
oligo
Microarray
updated 14.1 years ago by
Ben Bolstad
★ 1.2k • written 14.1 years ago by
Benilton Carvalho
★ 4.3k
0
votes
1
reply
695
views
reference on package affyPLM, fitPLM
affyPLM
affyPLM
19.5 years ago
Fangxin Hong
▴ 810
0
votes
1
reply
917
views
Quality control on Human Affymetrix Exon microarrays
affyPLM
xps
affyPLM
xps
updated 13.6 years ago by
cstrato
★ 3.9k • written 13.6 years ago by
branislav misovic
▴ 120
0
votes
3
replies
1.0k
views
AffyPLM
affyPLM
affyPLM
18.7 years ago
lucia ¿?
▴ 50
0
votes
2
replies
1.3k
views
Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1
affy
gcrma
matchprobes
affyPLM
affyio
affy
gcrma
matchprobes
affyPLM
affyio
updated 17.8 years ago by
zph@herald.ox.ac.uk
▴ 50 • written 17.8 years ago by
Michael Oldham
▴ 20
0
votes
1
reply
1.2k
views
NUSE lmFit fitPLM
Microarray
limma
affyPLM
updated 8.2 years ago by
Gordon Smyth
50k • written 12.0 years ago by
BIll Fends
▴ 10
0
votes
3
replies
1.5k
views
ExpressionSet, fitPLM confusion
cdf
probe
gcrma
matchprobes
affyPLM
affyio
cdf
probe
gcrma
matchprobes
affyPLM
affyio
updated 17.3 years ago by
Wolfgang Huber
★ 13k • written 17.3 years ago by
Georg Otto
▴ 510
0
votes
1
reply
1.3k
views
package \"affyPLM\" install errors on linux
affyPLM
affyPLM
updated 10.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.7 years ago by
Guest User
★ 13k
0
votes
2
replies
1.4k
views
SCAN.UPC vs NUSE
affy
affyPLM
SCAN.UPC
affy
affyPLM
SCAN.UPC
updated 10.5 years ago by
Stephen Piccolo
▴ 590 • written 10.5 years ago by
Leif Peterson
▴ 10
0
votes
2
replies
965
views
Saving all AffyPLM residual plots to disk
affyPLM
affyPLM
updated 10.5 years ago by
James W. MacDonald
65k • written 10.5 years ago by
lep
▴ 90
0
votes
4
replies
1.4k
views
affyPLM crashing R
affyPLM
Harshlight
affyPLM
Harshlight
updated 10.3 years ago by
Wolfgang Huber
★ 13k • written 10.3 years ago by
Guest User
★ 13k
0
votes
3
replies
1.3k
views
Is a subset of my arrays from degraded RNA?
Microarray
GO
Clustering
affy
affyPLM
simpleaffy
Microarray
GO
Clustering
affy
affyPLM
9.7 years ago
Peter Davidsen
▴ 210
50 results • Page
1 of 1
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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