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Showing :
affy
•
reset
0
votes
0
replies
1.1k
views
Question on limma design matrix
affy
affy
16.8 years ago
Sim, Fraser
▴ 350
0
votes
3
replies
1.7k
views
Probe-level rma vs. gene-level rma in "Affy"
affy
affy
updated 16.8 years ago by
James W. MacDonald
68k • written 16.8 years ago by
Skewes,Aaron
▴ 60
0
votes
8
replies
2.0k
views
affylmGUI segfault on "pd.ragene.1.0.st.v1"
Normalization
GO
cdf
affy
affylmGUI
Normalization
GO
cdf
affy
affylmGUI
updated 16.8 years ago by
Wolfgang Huber
★ 13k • written 16.8 years ago by
Harry Mangalam
▴ 70
0
votes
9
replies
2.8k
views
affy package RMA results difference from R2.5 to R2.8
affy
affyio
affy
affyio
updated 16.9 years ago by
balag Ganesan
▴ 140 • written 16.9 years ago by
He, Yiwen NIH/CIT
▴ 360
0
votes
0
replies
828
views
Bioc-devel Digest, Vol 57, Issue 4
Annotation
Normalization
GO
affy
PROcess
Annotation
Normalization
GO
affy
PROcess
16.9 years ago
rcaloger
▴ 500
0
votes
1
reply
1.6k
views
A CGH platform question
SNP
Genetics
Coverage
CGH
affy
SNP
Genetics
Coverage
CGH
affy
updated 16.9 years ago by
Henrik Bengtsson
★ 2.4k • written 16.9 years ago by
Johan Lindberg
▴ 70
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
16.9 years ago
Dick Beyer
★ 1.4k
0
votes
1
reply
842
views
Applying bioconductor functions to files in different Windows directories
annotate
affy
annotate
affy
updated 16.9 years ago by
Mark Robinson
★ 1.1k • written 16.9 years ago by
Ruppert Valentino
▴ 270
0
votes
2
replies
3.6k
views
biomaRt 3'UTR coordinates
affy
affy
16.9 years ago
Iain Gallagher
▴ 930
0
votes
2
replies
1.3k
views
Normalizing data (that is not in microarray "format")
affy
affy
updated 16.9 years ago by
Sean Davis
21k • written 16.9 years ago by
Emmanuel Levy
▴ 270
0
votes
0
replies
1.4k
views
Affymetrix Array Rat Gene 1.0 ST - some annotation challenges
Annotation
Normalization
probe
affy
PROcess
oligo
exonmap
Annotation
Normalization
probe
16.9 years ago
Alexander C Cambon
▴ 30
0
votes
2
replies
1.3k
views
makecdfenv crashes
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 16.9 years ago by
James W. MacDonald
68k • written 16.9 years ago by
Skewes,Aaron
▴ 60
0
votes
4
replies
1.9k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation
cdf
probe
affy
affyPLM
Annotation
cdf
probe
affy
affyPLM
updated 16.9 years ago by
James W. MacDonald
68k • written 16.9 years ago by
Peter White
▴ 130
0
votes
2
replies
2.0k
views
Custom CDF files
Annotation
GO
cdf
affy
PROcess
oligo
pdInfoBuilder
Annotation
GO
cdf
affy
PROcess
updated 16.9 years ago by
Mark Robinson
★ 1.1k • written 16.9 years ago by
Edward Oakeley
▴ 20
0
votes
1
reply
1.6k
views
Prokaryotic_Rhodobacter capsulatus GEP
Epigenetics
cdf
affy
makecdfenv
plier
affxparser
preprocessCore
Epigenetics
cdf
affy
updated 16.9 years ago by
dorothyc
▴ 140 • written 16.9 years ago by
James W. MacDonald
68k
0
votes
0
replies
850
views
Custom CDF files
Annotation
GO
cdf
affy
PROcess
Annotation
GO
cdf
affy
PROcess
16.9 years ago
Edward Oakeley
▴ 20
0
votes
1
reply
1.1k
views
human exon array 1.0ST, exonmap, exon.pmcdf troubles
cdf
affy
cdf
affy
17.0 years ago
Tobias Straub
▴ 430
0
votes
2
replies
1.9k
views
Using GenomeGraphs effectively for generating publication quality pictures
affy
biomaRt
ideogram
GenomeGraphs
affy
biomaRt
ideogram
GenomeGraphs
updated 17.0 years ago by
steffen@stat.Berkeley.EDU
▴ 600 • written 17.0 years ago by
Daren Tan
▴ 190
0
votes
2
replies
2.0k
views
Can't load annotations with lumi
Microarray
OneChannel
Annotation
Normalization
probe
Biobase
annotate
genefilter
affy
vsn
updated 17.0 years ago by
Pan Du
★ 1.2k • written 17.0 years ago by
Steve Taylor
▴ 280
0
votes
1
reply
1.3k
views
some help for Limma Factorial design for two color data.
Microarray
affy
limma
Microarray
affy
limma
updated 17.0 years ago by
De-Jian ZHAO
▴ 240 • written 17.0 years ago by
Adrian Johnson
▴ 330
0
votes
0
replies
800
views
Continued problems with pdInfoBuilder (Matt Settles)
affy
pdInfoBuilder
affy
pdInfoBuilder
17.0 years ago
Matt Settles
▴ 70
0
votes
1
reply
1.3k
views
Quantile normalization of MiRNA array data
miRNA
affy
miRNA
affy
updated 17.0 years ago by
Henrik Bengtsson
★ 2.4k • written 17.0 years ago by
Matthew Neville
▴ 30
0
votes
2
replies
1.6k
views
using GSEAlm with GO geneSetCollections
GO
affy
goTools
Category
GSEABase
GSEAlm
GO
affy
goTools
Category
GSEABase
GSEAlm
updated 17.0 years ago by
Dykema, Karl
▴ 90 • written 17.0 years ago by
Mark W Kimpel
▴ 830
0
votes
4
replies
1.9k
views
CDF issue
Annotation
Cancer
cdf
annotate
affy
Annotation
Cancer
cdf
annotate
affy
17.0 years ago
Mathe, Ewy NIH/NCI [F]
▴ 40
0
votes
2
replies
1.3k
views
PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays
affy
oligo
affy
oligo
updated 17.0 years ago by
Sean Davis
21k • written 17.0 years ago by
Mary Putt
▴ 100
0
votes
1
reply
1.5k
views
PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays
affy
oligo
affy
oligo
updated 17.0 years ago by
Sean Davis
21k • written 17.0 years ago by
Mary Putt
▴ 100
0
votes
4
replies
1.5k
views
applicability of tilingArray package
Normalization
Yeast
affy
tilingArray
Normalization
Yeast
affy
tilingArray
updated 17.0 years ago by
Wolfgang Huber
★ 13k • written 17.0 years ago by
Michael Palumbo
▴ 50
0
votes
5
replies
1.6k
views
missing functions in affy package
affy
affy
updated 17.0 years ago by
Henrik Bengtsson
★ 2.4k • written 17.0 years ago by
Rachael Hageman
▴ 20
0
votes
1
reply
1.0k
views
Combining old Affy arrays for limma
rat2302
rgu34a
rgu34b
rgu34c
affy
limma
Category
rat2302
rgu34a
rgu34b
rgu34c
affy
updated 17.0 years ago by
Sean Davis
21k • written 17.0 years ago by
james perkins
▴ 300
0
votes
8
replies
2.3k
views
Annotation packages
Annotation
GO
hgu95av2
affy
limma
Annotation
GO
hgu95av2
affy
limma
updated 17.0 years ago by
Sean Davis
21k • written 17.0 years ago by
Sim, Fraser
▴ 350
0
votes
1
reply
2.0k
views
problem with AnnotationDbi
ChipName
db0
affy
Category
AnnotationDbi
ChipName
db0
affy
Category
AnnotationDbi
updated 17.0 years ago by
Hervé Pagès
16k • written 17.0 years ago by
Mark W Kimpel
▴ 830
0
votes
1
reply
1.2k
views
Problem installing 'affy' with R-2.8.0
affy
affy
updated 17.0 years ago by
Martin Morgan
25k • written 17.0 years ago by
Mizanur Khondoker
▴ 10
0
votes
0
replies
896
views
pmcorrect.mas
affy
affy
17.0 years ago
Matthias Kohl
▴ 160
0
votes
1
reply
1.3k
views
Extreme weighting values using arrayWeights
Clustering
affy
limma
Clustering
affy
limma
updated 17.0 years ago by
Matt Ritchie
▴ 50 • written 17.1 years ago by
james perkins
▴ 300
0
votes
5
replies
2.7k
views
GOstats: Listing genes from hyperGTest
Annotation
GO
probe
affy
Annotation
GO
probe
affy
17.0 years ago
Tim Smith
★ 1.1k
0
votes
5
replies
2.1k
views
newbie problems with AnnBuilder
Annotation
Organism
cdf
probe
affy
AnnBuilder
Annotation
Organism
cdf
probe
affy
updated 17.1 years ago by
Marc Carlson
★ 7.2k • written 17.1 years ago by
Mark W Kimpel
▴ 830
0
votes
3
replies
1.7k
views
help with using Category package with makecdfenv built Gene ST package
GO
cdf
affy
limma
Category
GO
cdf
affy
limma
Category
updated 17.1 years ago by
rgentleman
★ 5.5k • written 17.1 years ago by
Mark W Kimpel
▴ 830
0
votes
0
replies
1.0k
views
limma: Combining probe level data prior to fitting
Microarray
Preprocessing
Regression
Yeast
probe
affy
limma
Microarray
Preprocessing
Yeast
17.1 years ago
Alex Gutteridge
▴ 650
0
votes
1
reply
804
views
help with using pdInfoBuilder and oligo for Affy Gene Set arrays
affy
oligo
affy
oligo
updated 17.1 years ago by
James W. MacDonald
68k • written 17.1 years ago by
Mark W Kimpel
▴ 830
0
votes
1
reply
1.2k
views
error while using oligo to build a custom affy cdf
BiocViews
cdf
affy
biocViews
BiocViews
BiocViews
cdf
affy
biocViews
updated 17.1 years ago by
James W. MacDonald
68k • written 17.1 years ago by
Mark W Kimpel
▴ 830
0
votes
4
replies
2.5k
views
topGO problem
GO
cdf
affy
topGO
GO
cdf
affy
topGO
17.1 years ago
Iain Gallagher
▴ 930
0
votes
1
reply
723
views
asking with problems with affymetrix data
affy
limma
affy
limma
updated 17.1 years ago by
Sean Davis
21k • written 17.1 years ago by
manzofabio@libero.it
▴ 10
0
votes
3
replies
1.2k
views
gene count in a GO term
affy
affy
17.1 years ago
Shi, Tao
▴ 720
0
votes
1
reply
1.1k
views
How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
Cancer
hgu95av2
affy
Cancer
hgu95av2
affy
updated 17.1 years ago by
Saurin D. Jani
▴ 360 • written 17.1 years ago by
Martin Morgan
25k
0
votes
1
reply
926
views
How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
affy
affy
updated 17.1 years ago by
Sean Davis
21k • written 17.1 years ago by
Saurin D. Jani
▴ 360
0
votes
0
replies
1.1k
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
17.1 years ago
Richard Friedman
★ 2.0k
0
votes
2
replies
1.5k
views
biomart doesn't annotate all the genes queried -CEACAM6
Cancer
hgu133plus2
annotate
affy
biomaRt
Cancer
hgu133plus2
annotate
affy
biomaRt
17.2 years ago • updated 17.1 years ago
Julian Lee
▴ 140
0
votes
0
replies
1.1k
views
Sc03b_MR_v04 CDF package
Annotation
probe
affy
Annotation
probe
affy
17.1 years ago
Williams, Alan
▴ 40
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 17.2 years ago by
Sean Davis
21k • written 17.2 years ago by
Ruppert Valentino
▴ 270
0
votes
0
replies
932
views
Pd info package affy 10K array
Microarray
Annotation
Cancer
cdf
probe
affy
Microarray
Annotation
Cancer
cdf
probe
affy
17.2 years ago
Henrik Bengtsson
★ 2.4k
1,805 results • Page
14 of 37
Recent ...
Replies
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Kevin Blighe
★ 4.0k
Hello Matthew, Thanks for the detailed description-this sounds like a classic challenge in sncRNA analysis, where piRNAs (and other tsRN…
Answer: VariantAnnotation does escape = within header string quotes
by
Kevin Blighe
★ 4.0k
Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
Answer: Setting up a DESeq2 Design with Paired Data
by
Kevin Blighe
★ 4.0k
Hello, Your design formula looks mostly correct to me, but I believe that `vessel_n` should be `replicate` (or whatever unique identifie…
Comment: Failure to download resources (MeSHDb) from AnnotationHub
by
Steve Lianoglou
★ 13k
That fixed it, thanks Lori!
Comment: Suppress warning in RHDF5 write
by
nicolas.lhuillier
• 0
Thanks a lot for the quick and effective reply. I had tried "suppressWarnings" but not "suppressMessages".
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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shepherl
4.2k
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to
James W. MacDonald
68k
Popular Question
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Daniel Cameron
▴ 40
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Peter Hickey
▴ 760
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