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gcrma
•
reset
0
votes
0
replies
1.1k
views
gcrma on affy xlaevis arrays
GO
affy
gcrma
GO
affy
gcrma
14.7 years ago
Tobias Straub
▴ 10
0
votes
3
replies
1.5k
views
Problem using justGCRMA
gcrma
gcrma
updated 14.7 years ago by
James W. MacDonald
68k • written 14.7 years ago by
Antonio Mendes
▴ 10
0
votes
1
reply
1.2k
views
customCDF name not recognized and switched to Affy CDF
cdf
affy
gcrma
cdf
affy
gcrma
updated 14.7 years ago by
James W. MacDonald
68k • written 14.7 years ago by
Yair Benita
▴ 80
0
votes
3
replies
1.3k
views
Creating 2 Gaussian Probability Density Function
gcrma
gcrma
updated 14.7 years ago by
Matthew McCall
▴ 830 • written 14.7 years ago by
viritha kaza
▴ 580
0
votes
2
replies
1.7k
views
gcrma - u133aaofav2probe error
Microarray
gcrma
marray
Microarray
gcrma
marray
updated 14.8 years ago by
James W. MacDonald
68k • written 14.8 years ago by
Myrto Kostadima
▴ 10
0
votes
3
replies
1.8k
views
GCRMA: feature request
GO
Regression
probe
gcrma
frma
GO
Regression
probe
gcrma
frma
updated 15.0 years ago by
Björn Usadel
▴ 250 • written 15.0 years ago by
Guido Hooiveld
★ 4.1k
0
votes
1
reply
2.1k
views
Help with GSEA package
hu6800
cdf
genefilter
multtest
affy
gcrma
siggenes
annaffy
GSEABase
hu6800
cdf
multtest
updated 15.1 years ago by
Martin Morgan
25k • written 15.1 years ago by
Jillian Rowe
▴ 20
0
votes
1
reply
957
views
gene expression set using KEGG
gcrma
gcrma
updated 15.1 years ago by
Martin Morgan
25k • written 15.1 years ago by
Peevi Ijkl
▴ 170
0
votes
10
replies
2.3k
views
Is GCRMA influenced by lexicographical order?
probe
gcrma
probe
gcrma
updated 15.2 years ago by
Wolfgang Huber
★ 13k • written 15.2 years ago by
markus.boenn
▴ 50
0
votes
1
reply
768
views
help with normalization
gcrma
gcrma
updated 15.3 years ago by
Richard Friedman
★ 2.0k • written 15.3 years ago by
Casper Shyr
▴ 140
0
votes
1
reply
1.2k
views
gcrma hugene10st array
gcrma
gcrma
updated 15.3 years ago by
Zhijin Wu
▴ 260 • written 15.3 years ago by
Andrew Einhorn
▴ 80
0
votes
1
reply
1.6k
views
gcrma vs rma
Microarray
qPCR
probe
ROC
limma
gcrma
Microarray
qPCR
probe
ROC
limma
gcrma
updated 15.4 years ago by
Zhijin Wu
▴ 260 • written 15.4 years ago by
Lucia Peixoto
▴ 330
0
votes
0
replies
1.3k
views
Different result from gcrma function by using command line gcrma, affylmGUI and oneChannelGUI.
gcrma
affylmGUI
oneChannelGUI
gcrma
affylmGUI
oneChannelGUI
15.4 years ago
Lin Ying
▴ 10
0
votes
2
replies
1.1k
views
Problem with gcrma
affy
gcrma
affy
gcrma
updated 15.6 years ago by
Paul Williams
▴ 10 • written 15.6 years ago by
Casper Shyr
▴ 140
0
votes
0
replies
1.5k
views
Basic Question about gcrma & exporting to excel > (command not working)
Microarray
affy
gcrma
oligo
arrayQualityMetrics
DECIPHER
Microarray
affy
gcrma
oligo
15.6 years ago
Dick Beyer
★ 1.4k
0
votes
5
replies
1.8k
views
Imitating Affy's own steps
Microarray
Normalization
GO
Preprocessing
gcrma
Microarray
Normalization
GO
Preprocessing
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
Timothy Wu
▴ 120
0
votes
4
replies
1.4k
views
GCRMA Normalization Differences between Windows and MAC
Normalization
gcrma
Normalization
gcrma
updated 15.8 years ago by
Zhijin Wu
▴ 260 • written 15.8 years ago by
martin martinez
▴ 10
0
votes
1
reply
987
views
Xlaevis probe sequence file for gcRMA not found.
xenopuslaevis
probe
gcrma
xenopuslaevis
probe
gcrma
updated 15.9 years ago by
James W. MacDonald
68k • written 15.9 years ago by
Naoki Irie
▴ 20
0
votes
1
reply
1.1k
views
FW: Problem in masking individual probes to calculate expression values
cdf
probe
gcrma
cdf
probe
gcrma
updated 15.9 years ago by
Memon, Farhat N
▴ 50 • written 15.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
4
replies
1.4k
views
Discrepancy on results from gcrma function and justGCRMA
gcrma
GLAD
gcrma
GLAD
updated 15.9 years ago by
James W. MacDonald
68k • written 15.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
2
replies
1.1k
views
Improvements on GCRMA function
gcrma
gcrma
updated 15.9 years ago by
Zhijin Wu
▴ 260 • written 15.9 years ago by
Javier Pérez Florido
▴ 840
0
votes
1
reply
934
views
FW: Problem in masking individual probes to calculate expression values
probe
gcrma
probe
gcrma
updated 16.0 years ago by
Jenny Drnevich
★ 2.0k • written 16.0 years ago by
Memon, Farhat N
▴ 50
0
votes
4
replies
1.2k
views
help needed for GCRMA
gcrma
gcrma
updated 16.0 years ago by
James W. MacDonald
68k • written 16.0 years ago by
Memon, Farhat N
▴ 50
0
votes
2
replies
1.6k
views
Fixing brainarray repository link for mac os x
Annotation
GO
CustomCDF
cdf
gcrma
Annotation
GO
CustomCDF
cdf
gcrma
updated 16.1 years ago by
James W. MacDonald
68k • written 16.1 years ago by
Yair Benita
▴ 80
0
votes
5
replies
2.5k
views
GCRMA Error
cdf
gcrma
cdf
gcrma
updated 16.2 years ago by
Zhijin Wu
▴ 260 • written 16.2 years ago by
Denise Mauldin
▴ 50
0
votes
0
replies
685
views
Discrepancy on results from gcrma function and justGCRMA
gcrma
gcrma
16.2 years ago
Jin
▴ 10
0
votes
0
replies
996
views
Expression values from gcRMA are different than before
gcrma
affylmGUI
gcrma
affylmGUI
16.3 years ago
Glyn Bradley
▴ 40
0
votes
2
replies
1.4k
views
about citrus chip
probe
affy
gcrma
probe
affy
gcrma
updated 16.3 years ago by
James W. MacDonald
68k • written 16.3 years ago by
yuduanding
▴ 40
0
votes
2
replies
1.4k
views
preprocessing Affymetrix with threestep and expresso
Microarray
Normalization
Preprocessing
affy
gcrma
Microarray
Normalization
Preprocessing
updated 16.4 years ago by
cstrato
★ 3.9k • written 16.4 years ago by
Javier Pérez Florido
▴ 840
0
votes
0
replies
865
views
Different gcrma output values after upgrade BioC 2.0 -> 2.4
Microarray
Normalization
GO
hgu133plus2
rgu34a
probe
gcrma
Microarray
Normalization
GO
16.4 years ago
Rullmann, J.A.C. Ton
▴ 40
0
votes
1
reply
892
views
Different gcrma output values after upgrade BioC 2.0 -> 2.4
probe
gcrma
probe
gcrma
updated 16.4 years ago by
Zhijin Wu
▴ 260 • written 16.4 years ago by
Rullmann, J.A.C. Ton
▴ 40
0
votes
2
replies
1.5k
views
preprocessing Affymetrix with threestep and expresso
Microarray
Normalization
Preprocessing
gcrma
Microarray
Normalization
Preprocessing
gcrma
updated 16.4 years ago by
Laurent Gautier
★ 2.3k • written 16.4 years ago by
Javier Pérez Florido
▴ 840
0
votes
0
replies
873
views
background correction on PM only: compute.affinities2()
affy
gcrma
affy
gcrma
16.5 years ago
Marianne Tuefferd
▴ 20
0
votes
1
reply
1.0k
views
gcrma and unable to access brainarray.mbni.med.umich.edu...
GO
gcrma
GO
gcrma
updated 16.7 years ago by
James W. MacDonald
68k • written 16.7 years ago by
Loren Engrav
★ 1.0k
0
votes
1
reply
1.4k
views
justGCRMA problem :(
GO
Cancer
gcrma
matchprobes
PROcess
affyio
GO
Cancer
gcrma
matchprobes
PROcess
affyio
updated 16.8 years ago by
Jacek Nowak
▴ 20 • written 16.9 years ago by
Martin Morgan
25k
0
votes
0
replies
1.3k
views
affyPLM QC vignette is missing...
probe
Biobase
affy
gcrma
matchprobes
affyPLM
probe
Biobase
affy
gcrma
matchprobes
16.9 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.4k
views
justGCRMA problem :(
GO
gcrma
matchprobes
PROcess
affyio
GO
gcrma
matchprobes
PROcess
affyio
16.9 years ago
Jacek Nowak
▴ 20
0
votes
1
reply
1.7k
views
Group-wise gcrma normalization
Microarray
Normalization
Clustering
zebrafish
probe
gcrma
Microarray
Normalization
probe
updated 16.9 years ago by
Kasper Daniel Hansen
★ 6.5k • written 16.9 years ago by
Jun Yin
▴ 30
0
votes
1
reply
1.3k
views
GCRMA: error / warning
probe
gcrma
probe
gcrma
updated 17.0 years ago by
Zhijin Wu
▴ 260 • written 17.0 years ago by
Guido Hooiveld
★ 4.1k
0
votes
3
replies
1.1k
views
discrepancies using different gcRMA
gcrma
gcrma
updated 17.1 years ago by
Zhijin Wu
▴ 260 • written 17.1 years ago by
Wen Huang
▴ 20
0
votes
0
replies
1.6k
views
sd==0 for some probesets when using gcrma
Microarray
Proteomics
Epigenetics
Normalization
GO
Cancer
hgu95av2
affy
graph
gcrma
GO
17.1 years ago
Dick Beyer
★ 1.4k
0
votes
2
replies
1.4k
views
Does old workspace work?
Regression
probe
gcrma
PROcess
maanova
Regression
probe
gcrma
PROcess
maanova
updated 17.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.2 years ago by
Loren Engrav
★ 1.0k
0
votes
1
reply
1.6k
views
How to definitely point to local mirror?
gcrma
gcrma
updated 17.2 years ago by
Hervé Pagès
16k • written 17.2 years ago by
Renaud Gaujoux
▴ 170
0
votes
0
replies
762
views
Discrepancy on results from gcrma function and justGCRMA
gcrma
gcrma
17.2 years ago
Jerry
▴ 10
0
votes
18
replies
3.6k
views
LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
Cancer
gcrma
LPE
affylmGUI
Cancer
gcrma
LPE
affylmGUI
updated 17.2 years ago by
Charlie Whittaker
▴ 70 • written 17.2 years ago by
Wolfgang Huber
★ 13k
0
votes
2
replies
1.4k
views
LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
Cancer
gcrma
LPE
Cancer
gcrma
LPE
updated 17.2 years ago by
Patrick Aboyoun
★ 1.6k • written 17.2 years ago by
Charlie Whittaker
▴ 70
0
votes
0
replies
1.2k
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
17.3 years ago
Richard Friedman
★ 2.0k
0
votes
1
reply
2.4k
views
what is the best baseline transformation method before clustering
GO
Clustering
probe
affy
gcrma
GeneSpring
GO
Clustering
probe
affy
gcrma
GeneSpring
updated 17.3 years ago by
Sean Davis
21k • written 17.3 years ago by
Ruppert Valentino
▴ 270
0
votes
0
replies
909
views
mu11ksuba + gcrma = error
mu11ksuba
cdf
gcrma
mu11ksuba
cdf
gcrma
17.3 years ago
Ido M. Tamir
▴ 150
0
votes
2
replies
3.2k
views
installing problem - preprocessCore, affy on linux platform
Biobase
genefilter
affy
vsn
gcrma
matchprobes
preprocessCore
Biobase
genefilter
affy
vsn
updated 17.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.4 years ago by
Read, Laura
▴ 20
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Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
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limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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