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affyplm
•
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0
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0
replies
902
views
(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM
fitPLM
hta2.0
7.7 years ago
Guido Hooiveld
★ 4.0k
1
vote
1
reply
1.0k
views
affyPLM boxplots for subset of samples
affyPLM
updated 7.9 years ago by
James W. MacDonald
66k • written 7.9 years ago by
Juliet Hannah
▴ 360
0
votes
1
reply
1.2k
views
NUSE lmFit fitPLM
Microarray
limma
affyPLM
updated 8.4 years ago by
Gordon Smyth
50k • written 12.1 years ago by
BIll Fends
▴ 10
1
vote
1
reply
2.3k
views
Computing NUSE and RLE scores
affyPLM
RLE
NUSE
updated 9.3 years ago by
Sean Davis
21k • written 9.3 years ago by
beverly893
▴ 10
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
9.8 years ago
Peter Davidsen
▴ 210
0
votes
4
replies
1.5k
views
affyPLM crashing R
affyPLM
Harshlight
affyPLM
Harshlight
updated 10.5 years ago by
Wolfgang Huber
★ 13k • written 10.5 years ago by
Guest User
★ 13k
0
votes
2
replies
1.0k
views
Saving all AffyPLM residual plots to disk
affyPLM
affyPLM
updated 10.6 years ago by
James W. MacDonald
66k • written 10.6 years ago by
lep
▴ 90
0
votes
2
replies
1.5k
views
SCAN.UPC vs NUSE
affy
affyPLM
SCAN.UPC
affy
affyPLM
SCAN.UPC
updated 10.7 years ago by
Stephen Piccolo
▴ 590 • written 10.7 years ago by
Leif Peterson
▴ 10
0
votes
1
reply
1.3k
views
package \"affyPLM\" install errors on linux
affyPLM
affyPLM
updated 10.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.9 years ago by
Guest User
★ 13k
0
votes
3
replies
2.1k
views
arrayQualityMetrics error on windows
affyPLM
affyPLM
11.7 years ago
Marcus Davy
▴ 390
0
votes
5
replies
1.1k
views
how to rank affy probesets by their probe-effect magnitude
probe
affy
affyPLM
probe
affy
affyPLM
updated 12.2 years ago by
James W. MacDonald
66k • written 12.2 years ago by
Robert Castelo
★ 3.3k
0
votes
0
replies
1.3k
views
arrayQualityMetrics package - bugs and errors
limma
affyPLM
convert
arrayQualityMetrics
limma
affyPLM
convert
arrayQualityMetrics
12.2 years ago
Wolfgang Huber
★ 13k
0
votes
4
replies
1.8k
views
arrayQualityMetrics package - bugs and errors
limma
affyPLM
arrayQualityMetrics
limma
affyPLM
arrayQualityMetrics
updated 12.3 years ago by
Wolfgang Huber
★ 13k • written 12.3 years ago by
Vladimir Krasikov
▴ 90
0
votes
4
replies
1.1k
views
MA plots for large number of arrays
affy
affyPLM
beadarray
lumi
affy
affyPLM
beadarray
lumi
updated 12.6 years ago by
boczniak767
▴ 720 • written 12.6 years ago by
Juliet Hannah
▴ 360
0
votes
0
replies
905
views
bitmap() extremely slow!
Microarray
affyPLM
Microarray
affyPLM
13.0 years ago
Groot, Philip de
▴ 630
0
votes
3
replies
1.1k
views
Images from exon arrays
affy
affyPLM
affy
affyPLM
13.7 years ago
Popovic, Jelena
▴ 20
0
votes
1
reply
954
views
Quality control on Human Affymetrix Exon microarrays
affyPLM
xps
affyPLM
xps
updated 13.7 years ago by
cstrato
★ 3.9k • written 13.7 years ago by
branislav misovic
▴ 120
0
votes
3
replies
1.5k
views
identical output plots for NUSE AND RLE
GO
Cancer
affyPLM
GO
Cancer
affyPLM
updated 13.9 years ago by
Paolo Innocenti
▴ 320 • written 13.9 years ago by
Richard Friedman
★ 2.0k
0
votes
0
replies
779
views
Loading workspace blocks generic function dispach
affyPLM
affyPLM
14.0 years ago
Eric Blanc
▴ 10
0
votes
0
replies
905
views
Problems in MAplot for affybatch objects
affy
affyPLM
affy
affyPLM
14.0 years ago
Ben Bolstad
★ 1.2k
0
votes
0
replies
863
views
Affy exon array equivalents of QC packages (affyPLM, arrayQualityMetrics & affyQCReport)
Cancer
affyPLM
affyQCReport
arrayQualityMetrics
Cancer
affyPLM
affyQCReport
14.1 years ago
Daniel Brewer
★ 1.9k
0
votes
0
replies
831
views
Accessing median and IQR values of MAplots
affyPLM
affyPLM
14.2 years ago
Javier Pérez Florido
▴ 840
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 14.2 years ago by
Ben Bolstad
★ 1.2k • written 14.2 years ago by
Benilton Carvalho
★ 4.3k
0
votes
2
replies
1.4k
views
objects masked from packages
affyPLM
affyPLM
updated 14.3 years ago by
James W. MacDonald
66k • written 14.3 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.2k
views
ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM
arrayQualityMetrics
affyPLM
arrayQualityMetrics
updated 14.6 years ago by
audrey
▴ 280 • written 14.6 years ago by
lohith madireddy
▴ 40
0
votes
0
replies
1.1k
views
affyPLM QC vignette is missing...
probe
Biobase
affy
gcrma
matchprobes
affyPLM
probe
Biobase
affy
gcrma
matchprobes
15.2 years ago
Jenny Drnevich
★ 2.0k
0
votes
5
replies
2.4k
views
error in ls() unused arguments
mouse4302
affyPLM
mouse4302
affyPLM
updated 15.3 years ago by
Laurent Gautier
★ 2.3k • written 15.3 years ago by
Wijchers, Patrick
▴ 40
0
votes
4
replies
1.5k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation
cdf
probe
affy
affyPLM
Annotation
cdf
probe
affy
affyPLM
updated 15.5 years ago by
James W. MacDonald
66k • written 15.5 years ago by
Peter White
▴ 130
0
votes
0
replies
914
views
spiked controls wrong order on samples wit 2 rounds of amplification normalize with GCRMA
Microarray
Cancer
affy
gcrma
affyPLM
Microarray
Cancer
affy
gcrma
affyPLM
15.7 years ago
Richard Friedman
★ 2.0k
0
votes
10
replies
1.7k
views
exonmap RMA function
Microarray
Cancer
affyPLM
exonmap
Microarray
Cancer
affyPLM
exonmap
updated 16.3 years ago by
Yuan Jian
▴ 250 • written 16.4 years ago by
Martin Morgan
25k
0
votes
0
replies
1.1k
views
MTP error
GO
Survival
multtest
affy
affydata
annaffy
affyPLM
affyio
GO
Survival
multtest
affy
16.5 years ago
Boel Brynedal
▴ 200
0
votes
1
reply
991
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 16.7 years ago by
Ben Bolstad
★ 1.2k • written 16.7 years ago by
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
1.0k
views
Questions about Affymetrix E. Coli arrays
Normalization
Cancer
affy
gcrma
affyPLM
Normalization
Cancer
affy
gcrma
affyPLM
16.8 years ago
Jenny Drnevich
★ 2.2k
0
votes
5
replies
1.9k
views
affyPLM - cant plot chip pseudo image
cdf
genefilter
affy
affydata
affyPLM
simpleaffy
affyio
cdf
genefilter
affy
affydata
updated 16.9 years ago by
James W. MacDonald
66k • written 16.9 years ago by
Tagett Rebecca
▴ 50
0
votes
0
replies
1.0k
views
Return of "I'm sorry, I do not know about chip type (foo)"
Survival
cdf
affydata
limma
gcrma
matchprobes
affyPLM
simpleaffy
Survival
cdf
affydata
16.9 years ago
Dave Jacoby
▴ 20
0
votes
0
replies
948
views
Normalization of 2 color Nimblegen array
cdf
affy
affyPLM
convert
oligo
makePlatformDesign
cdf
affy
affyPLM
convert
oligo
17.0 years ago
dhruv pant
▴ 30
0
votes
9
replies
1.9k
views
problem with duplicateCorrelation and ExpressionSet objects
GO
Survival
cdf
Biobase
graph
limma
gcrma
annaffy
affyPLM
simpleaffy
biomaRt
Category
updated 17.0 years ago by
Seth Falcon
★ 7.4k • written 17.0 years ago by
Jenny Drnevich
★ 2.2k
0
votes
4
replies
1.8k
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 17.1 years ago by
Ben Bolstad
★ 1.2k • written 17.1 years ago by
Allen Day
▴ 30
0
votes
2
replies
1.7k
views
"AveExp" column has dissappeared from limma topTable
GO
Survival
annotate
geneplotter
affydata
limma
annaffy
affyPLM
GO
Survival
annotate
updated 17.1 years ago by
Gordon Smyth
50k • written 17.1 years ago by
Marcus Davy
▴ 680
0
votes
0
replies
990
views
Analysis with MBNI re-mapped (custom) CDF files
Microarray
Clustering
cdf
probe
affy
affyPLM
mmgmos
Microarray
Clustering
cdf
probe
17.3 years ago
Richard Pearson
▴ 390
0
votes
4
replies
1.5k
views
Problems with the size of the plots obtained with AffyPLM
cdf
affy
gcrma
affyPLM
affyio
cdf
affy
gcrma
affyPLM
affyio
updated 17.4 years ago by
Oosting, J. PATH
▴ 550 • written 17.4 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
11
replies
2.7k
views
trouble hacking plotPCA
GO
Survival
Biobase
genefilter
affy
affydata
graph
limma
gcrma
matchprobes
affyPLM
RBGL
updated 17.4 years ago by
Rustici, Gabriella NIH/NCI [F]
▴ 10 • written 17.4 years ago by
Jenny Drnevich
★ 2.2k
0
votes
3
replies
1.6k
views
ExpressionSet, fitPLM confusion
cdf
probe
gcrma
matchprobes
affyPLM
affyio
cdf
probe
gcrma
matchprobes
affyPLM
affyio
updated 17.4 years ago by
Wolfgang Huber
★ 13k • written 17.4 years ago by
Georg Otto
▴ 510
0
votes
12
replies
2.0k
views
Some Genefilter questions
GO
Survival
cdf
genefilter
geneplotter
tkWidgets
affy
affydata
widgetTools
gcrma
affyPLM
updated 17.5 years ago by
rgentleman
★ 5.5k • written 17.5 years ago by
Amy Mikhail
▴ 460
0
votes
2
replies
2.9k
views
Error in function (classes, fdef, mtable)
cdf
genefilter
reposTools
gcrma
matchprobes
affyPLM
simpleaffy
affyio
cdf
genefilter
updated 17.5 years ago by
Seth Falcon
★ 7.4k • written 17.5 years ago by
D.Enrique ESCOBAR ESPINOZA
▴ 360
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 17.7 years ago by
Ben Bolstad
★ 1.2k • written 17.7 years ago by
k. brand
▴ 420
0
votes
0
replies
970
views
method for removing consistent technical bias?
affy
affydata
vsn
limma
gcrma
matchprobes
affyPLM
affyio
affy
affydata
vsn
limma
gcrma
17.7 years ago
k. brand
▴ 420
0
votes
2
replies
975
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf
gcrma
matchprobes
affyPLM
affyio
cdf
gcrma
matchprobes
affyPLM
affyio
updated 17.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.7 years ago by
k. brand
▴ 420
0
votes
0
replies
943
views
4 replicates, of 3 tissues- one good hyb (2xreps), one bad hyb (2xreps). Best way forward?
qPCR
affy
affydata
vsn
limma
gcrma
matchprobes
affyPLM
affyio
BRAIN
qPCR
affy
affydata
17.7 years ago
k. brand
▴ 420
0
votes
2
replies
891
views
loading affyPLM with R 2.4.
affyPLM
affyPLM
updated 17.7 years ago by
Ben Bolstad
★ 1.2k • written 17.7 years ago by
Oliver Hartmann
▴ 20
50 results • Page
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Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
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Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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