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cdf
•
reset
1
vote
4
replies
4.7k
views
Affymetrix Human Gene 1.0 ST Array
Infrastructure
cdf
probe
affy
Infrastructure
cdf
probe
affy
16.0 years ago
Hans-Ulrich Klein
▴ 330
0
votes
4
replies
4.4k
views
Bioconductor with Affymetrix Mouse Gene 1.0 ST
Annotation
cdf
PROcess
safe
Annotation
cdf
PROcess
safe
13.1 years ago
M. Emily Merrill
▴ 20
0
votes
1
reply
4.3k
views
Error in getCdfInfo(object)
cdf
cdf
updated 14.1 years ago by
James W. MacDonald
65k • written 14.1 years ago by
Arun A K
▴ 20
3
votes
7
replies
4.2k
views
miRNA microarray analysis
microarray
cdf
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
aswathym
▴ 10
0
votes
8
replies
4.0k
views
error ReadAffy
Arabidopsis thaliana
cdf
affy
gcrma
PROcess
oligo
xps
Arabidopsis thaliana
cdf
affy
xps
updated 6.1 years ago by
joseph.a.white1
• 0 • written 10.2 years ago by
nooshin
▴ 300
0
votes
2
replies
3.6k
views
justRMA couldn't obtain CDF environment
cdf
cdf
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Li Liu
▴ 100
0
votes
19
replies
3.4k
views
Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
Annotation
cdf
Annotation
cdf
updated 11.9 years ago by
James W. MacDonald
65k • written 11.9 years ago by
Andreas Heider
▴ 340
0
votes
3
replies
3.4k
views
Installation of XCMS / mzR failed
cdf
xcms
BiocInstaller
cdf
xcms
BiocInstaller
updated 11.7 years ago by
James W. MacDonald
65k • written 11.7 years ago by
Johannes Raffler
▴ 20
0
votes
6
replies
3.3k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation
GO
Survival
ExperimentData
cdf
DynDoc
genefilter
geneplotter
multtest
affy
GO
updated 16.7 years ago by
Weiyin Zhou
▴ 220 • written 16.7 years ago by
Jenny Drnevich
★ 2.2k
1
vote
3
replies
2.9k
views
How to analyse clariom d human files
limma
pdinfobuilder
affy
cdf
7.1 years ago
yusuf.khan
▴ 10
1
vote
4
replies
2.9k
views
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA
Microarray
cdf
makecdfenv
miRNA
Microarray
cdf
makecdfenv
updated 10.3 years ago by
James W. MacDonald
65k • written 10.3 years ago by
Guest User
★ 13k
0
votes
1
reply
2.9k
views
Array Express HuGene-1_1-st-v1 CDF problem
cdf
microarray
affy
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
mlyall
• 0
0
votes
2
replies
2.9k
views
Error in function (classes, fdef, mtable)
cdf
genefilter
reposTools
gcrma
matchprobes
affyPLM
simpleaffy
affyio
cdf
genefilter
updated 17.4 years ago by
Seth Falcon
★ 7.4k • written 17.4 years ago by
D.Enrique ESCOBAR ESPINOZA
▴ 360
0
votes
10
replies
2.7k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray
Normalization
cdf
oligo
DTA
Microarray
Normalization
cdf
oligo
DTA
updated 14.2 years ago by
Benilton Carvalho
★ 4.3k • written 14.2 years ago by
Mikhail Pachkov
▴ 110
0
votes
8
replies
2.7k
views
Error in setQCEnvironment(cdfn)
cdf
cdf
updated 11.6 years ago by
James W. MacDonald
65k • written 11.6 years ago by
suparna mitra
▴ 290
0
votes
1
reply
2.7k
views
Analysis of Human Gene 1.1 ST Array
Microarray
cdf
affy
PROcess
oligo
xps
Microarray
cdf
affy
PROcess
oligo
xps
updated 10.5 years ago by
James W. MacDonald
65k • written 10.5 years ago by
Jerry Cholo
▴ 190
2
votes
2
replies
2.7k
views
Issue with 'Could not obtain CDF environment' after attempting to extract information out of an AffyBatch object
Affy
cdf
.cel
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
maxime.vanhaeverbeke
• 0
2
votes
4
replies
2.7k
views
makePdInfoPackage for Primeview arrays
BiocViews
Annotation
Cancer
Organism
cdf
probe
affy
biocViews
BiocViews
BiocViews
Cancer
updated 10.9 years ago by
cstrato
★ 3.9k • written 10.9 years ago by
Max Kauer
▴ 140
0
votes
9
replies
2.6k
views
frma and alternative CDFs
GO
cdf
frma
BRAIN
GO
cdf
frma
BRAIN
updated 9.8 years ago by
Matthew McCall
▴ 830 • written 9.8 years ago by
Guest User
★ 13k
0
votes
1
reply
2.6k
views
annotation package for HuEx-1_0-st-v1 platform instead of pd.huex.1.0.st.v1
Microarray
Annotation
hgu133a
hgu133plus2
cdf
Microarray
Annotation
hgu133a
hgu133plus2
updated 10.4 years ago by
cstrato
★ 3.9k • written 10.4 years ago by
Rahmatallah, Yasir
▴ 10
0
votes
3
replies
2.5k
views
Affymetrix CEL files
cdf
GWASTools
cdf
GWASTools
updated 11.0 years ago by
James W. MacDonald
65k • written 11.0 years ago by
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
2.5k
views
affy hugene 2.1 st
cdf
cdf
updated 11.7 years ago by
Guest User
★ 13k • written 11.7 years ago by
Dario Greco
▴ 310
0
votes
5
replies
2.5k
views
Load CDF files for Affymetrix ST 2.0 microarrays
microarray
oligo
cdf
customcdf
updated 8.4 years ago by
Guido Hooiveld
★ 3.9k • written 8.4 years ago by
Nathaniel
▴ 20
0
votes
2
replies
2.5k
views
Processing array with R
cdf
software error
affy
R
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
Charlie
• 0
0
votes
5
replies
2.5k
views
GSVA questions
cdf
GSVA
cdf
GSVA
10.6 years ago
Guest User
★ 13k
0
votes
2
replies
2.4k
views
Importing CDF file for custom array using makecdfenv
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 17.7 years ago by
Michal Okoniewski
▴ 120 • written 17.7 years ago by
Ann Hess
▴ 340
0
votes
6
replies
2.4k
views
Library installation: odd error
cdf
probe
cdf
probe
updated 12.8 years ago by
Steve Lianoglou
★ 13k • written 12.8 years ago by
Michael Bauer
▴ 50
0
votes
0
replies
2.4k
views
[Fwd: Error (affy) loading 'listcel' and 'CDF.example']
cdf
affy
cdf
affy
21.8 years ago
Carleton Garrett
▴ 80
0
votes
8
replies
2.4k
views
CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?
miRNA
GO
cdf
affy
arrayQualityMetrics
miRNA
GO
cdf
affy
arrayQualityMetrics
updated 11.5 years ago by
James W. MacDonald
65k • written 11.5 years ago by
Stephen Turner
▴ 290
0
votes
9
replies
2.4k
views
using frma and brainarray cdf on exon arrays
cdf
affy
PROcess
oligo
xps
frma
cdf
affy
PROcess
oligo
xps
frma
updated 10.3 years ago by
Stephen Piccolo
▴ 590 • written 10.3 years ago by
Ty Thomson
▴ 100
0
votes
4
replies
2.4k
views
HGU95a and HGU95av2 with gcrma
hgu95a
hgu95av2
cdf
gcrma
hgu95a
hgu95av2
cdf
gcrma
updated 19.4 years ago by
Wolfgang Huber
★ 13k • written 19.4 years ago by
Vincent Detours
▴ 80
0
votes
1
reply
2.3k
views
affy - Anotation of Afymetrix PrimeView chipe
cdf
probe
affy
limma
cdf
probe
affy
limma
updated 10.5 years ago by
James W. MacDonald
65k • written 10.5 years ago by
Adam Olejnik
▴ 10
0
votes
6
replies
2.3k
views
CDF file for Mouse Gene 1.1 ST Array
cdf
cdf
updated 13.4 years ago by
Pascal Gellert
▴ 80 • written 13.4 years ago by
Lucia Peixoto
▴ 330
0
votes
0
replies
2.3k
views
comparing affymetrix and agilent microarray data
cdf
probe
affy
cdf
probe
affy
14.9 years ago
Jarek Bryk
▴ 110
0
votes
12
replies
2.3k
views
justRMA?
cdf
probe
cdf
probe
updated 11.4 years ago by
James W. MacDonald
65k • written 11.4 years ago by
Bhargavi Duvvuri
▴ 70
0
votes
13
replies
2.3k
views
arrayQualityMetrics error and question
cdf
arrayQualityMetrics
cdf
arrayQualityMetrics
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
David Westergaard
▴ 280
0
votes
4
replies
2.2k
views
.cel file processing is not working for an old array
cdf
PROcess
cdf
PROcess
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Maria Kesa
▴ 30
0
votes
2
replies
2.2k
views
Installing packages on R v2.13.2, OSX multiple warning messages
Annotation
cdf
probe
affy
gcrma
Annotation
cdf
probe
affy
gcrma
updated 12.5 years ago by
James W. MacDonald
65k • written 12.5 years ago by
Guest User
★ 13k
0
votes
2
replies
2.2k
views
make.cdf.package Error in copySubstitute
GO
cdf
Biobase
affy
GO
cdf
Biobase
affy
updated 10.1 years ago by
James W. MacDonald
65k • written 10.1 years ago by
matthew vitalone
▴ 30
0
votes
4
replies
2.2k
views
affyPara
cdf
affy
affyPara
cdf
affy
affyPara
13.6 years ago • updated 13.5 years ago
danieladna
▴ 110
0
votes
2
replies
2.2k
views
problem installing 'GLAD' package
cdf
GLAD
cdf
GLAD
13.4 years ago
Shenglin Zheng
▴ 20
0
votes
1
reply
2.2k
views
GWASTools
cdf
GWASTools
cdf
GWASTools
10.7 years ago
Stephanie M. Gogarten
▴ 870
0
votes
5
replies
2.1k
views
Affymetrix HT HG-U133+ PM Array Plate annotation data
Annotation
cdf
probe
Annotation
cdf
probe
updated 14.4 years ago by
Marc Carlson
★ 7.2k • written 14.4 years ago by
giacomo.tuana@unimib.it
▴ 40
0
votes
5
replies
2.1k
views
Analysing Human Gene ST 1.0 Arrays with oligo and oneChannelGUI yield different number of probesets
Preprocessing
cdf
oligo
oneChannelGUI
Preprocessing
cdf
oligo
oneChannelGUI
updated 14.5 years ago by
Benilton Carvalho
★ 4.3k • written 14.5 years ago by
Javier Pérez Florido
▴ 840
0
votes
1
reply
2.1k
views
CDF environment missing for HuGene-1_0-st-v1
cdf
cdf
updated 14.1 years ago by
James W. MacDonald
65k • written 14.1 years ago by
Legaie, Roxane
▴ 20
0
votes
12
replies
2.1k
views
Bioconductor - hugene10stv1cdf not available
cdf
cdf
14.0 years ago
Christoph Knapp
▴ 70
0
votes
3
replies
2.1k
views
ReadAffy Error
Annotation
ExperimentData
cdf
affy
affyio
Annotation
ExperimentData
cdf
affy
affyio
updated 16.7 years ago by
Sylvia.Merk@ukmuenster.de
▴ 60 • written 16.7 years ago by
Markus Schmidberger
▴ 380
0
votes
1
reply
2.1k
views
limma topTable with gene symbols in output: annotate problem
Annotation
cdf
probe
annotate
affy
limma
biomaRt
Annotation
cdf
probe
annotate
affy
updated 12.3 years ago by
Marc Carlson
★ 7.2k • written 12.3 years ago by
Stephen Turner
▴ 290
0
votes
2
replies
2.1k
views
Cannot open compressed file
Cancer
cdf
Cancer
cdf
updated 20.4 years ago by
rgentleman
★ 5.5k • written 20.4 years ago by
Simon, Richard NIH/NCI
▴ 20
0
votes
2
replies
2.0k
views
HGU133Plus2 CDF vs hgu133plus2hsentrezgcdf CDF (30% difference in results)
GO
hgu133plus2
cdf
affy
limma
updated 9.6 years ago by
Steve Lianoglou
★ 13k • written 9.6 years ago by
Guest User
★ 13k
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
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pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
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41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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by
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41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
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That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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