Showing : affy • reset
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Question on limma design matrix
affy affy
16.8 years ago Sim, Fraser ▴ 350
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3
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1.7k
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Probe-level rma vs. gene-level rma in "Affy"
affy affy
updated 16.8 years ago by 68k • written 16.8 years ago by ▴ 60
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8
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2.0k
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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 ★ 13k • written 16.8 years ago by ▴ 70
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affy package RMA results difference from R2.5 to R2.8
affy affyio affy affyio
updated 16.9 years ago by ▴ 140 • written 16.9 years ago by ▴ 360
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Bioc-devel Digest, Vol 57, Issue 4
Annotation Normalization GO affy PROcess Annotation Normalization GO affy PROcess
16.9 years ago rcaloger ▴ 500
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1
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1.6k
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A CGH platform question
SNP Genetics Coverage CGH affy SNP Genetics Coverage CGH affy
updated 16.9 years ago by ★ 2.4k • written 16.9 years ago by ▴ 70
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1.6k
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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
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1
reply
842
views
Applying bioconductor functions to files in different Windows directories
annotate affy annotate affy
updated 16.9 years ago by ★ 1.1k • written 16.9 years ago by ▴ 270
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2
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3.6k
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biomaRt 3'UTR coordinates
affy affy
16.9 years ago Iain Gallagher ▴ 930
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2
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1.3k
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Normalizing data (that is not in microarray "format")
affy affy
updated 16.9 years ago by 21k • written 16.9 years ago by ▴ 270
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0
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1.4k
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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
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2
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1.3k
views
makecdfenv crashes
cdf affy makecdfenv cdf affy makecdfenv
updated 16.9 years ago by 68k • written 16.9 years ago by ▴ 60
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4
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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 68k • written 16.9 years ago by ▴ 130
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2
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2.0k
views
Custom CDF files
Annotation GO cdf affy PROcess oligo pdInfoBuilder Annotation GO cdf affy PROcess
updated 16.9 years ago by ★ 1.1k • written 16.9 years ago by ▴ 20
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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 ▴ 140 • written 16.9 years ago by 68k
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0
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850
views
Custom CDF files
Annotation GO cdf affy PROcess Annotation GO cdf affy PROcess
16.9 years ago Edward Oakeley ▴ 20
0
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1
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1.1k
views
human exon array 1.0ST, exonmap, exon.pmcdf troubles
cdf affy cdf affy
17.0 years ago Tobias Straub ▴ 430
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2
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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 ▴ 600 • written 17.0 years ago by ▴ 190
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2
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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 ★ 1.2k • written 17.0 years ago by ▴ 280
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1
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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 ▴ 240 • written 17.0 years ago by ▴ 330
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0
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800
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Continued problems with pdInfoBuilder (Matt Settles)
affy pdInfoBuilder affy pdInfoBuilder
17.0 years ago Matt Settles ▴ 70
0
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1
reply
1.3k
views
Quantile normalization of MiRNA array data
miRNA affy miRNA affy
updated 17.0 years ago by ★ 2.4k • written 17.0 years ago by ▴ 30
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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 ▴ 90 • written 17.0 years ago by ▴ 830
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4
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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
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2
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1.3k
views
PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays
affy oligo affy oligo
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 100
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1
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1.5k
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PdInfobuilder: Preparing data from Affymetrix HuGene expression arrays
affy oligo affy oligo
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 100
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4
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1.5k
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applicability of tilingArray package
Normalization Yeast affy tilingArray Normalization Yeast affy tilingArray
updated 17.0 years ago by ★ 13k • written 17.0 years ago by ▴ 50
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5
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1.6k
views
missing functions in affy package
affy affy
updated 17.0 years ago by ★ 2.4k • written 17.0 years ago by ▴ 20
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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 21k • written 17.0 years ago by ▴ 300
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8
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2.3k
views
Annotation packages
Annotation GO hgu95av2 affy limma Annotation GO hgu95av2 affy limma
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 350
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1
reply
2.0k
views
problem with AnnotationDbi
ChipName db0 affy Category AnnotationDbi ChipName db0 affy Category AnnotationDbi
updated 17.0 years ago by 16k • written 17.0 years ago by ▴ 830
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1
reply
1.2k
views
Problem installing 'affy' with R-2.8.0
affy affy
updated 17.0 years ago by 25k • written 17.0 years ago by ▴ 10
0
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0
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896
views
pmcorrect.mas
affy affy
17.0 years ago Matthias Kohl ▴ 160
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1
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1.3k
views
Extreme weighting values using arrayWeights
Clustering affy limma Clustering affy limma
updated 17.0 years ago by ▴ 50 • written 17.1 years ago by ▴ 300
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5
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2.7k
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GOstats: Listing genes from hyperGTest
Annotation GO probe affy Annotation GO probe affy
17.0 years ago Tim Smith ★ 1.1k
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5
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2.1k
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newbie problems with AnnBuilder
Annotation Organism cdf probe affy AnnBuilder Annotation Organism cdf probe affy
updated 17.1 years ago by ★ 7.2k • written 17.1 years ago by ▴ 830
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3
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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 ★ 5.5k • written 17.1 years ago by ▴ 830
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0
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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
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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 68k • written 17.1 years ago by ▴ 830
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1
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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 68k • written 17.1 years ago by ▴ 830
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4
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2.5k
views
topGO problem
GO cdf affy topGO GO cdf affy topGO
17.1 years ago Iain Gallagher ▴ 930
0
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1
reply
723
views
asking with problems with affymetrix data
affy limma affy limma
updated 17.1 years ago by 21k • written 17.1 years ago by ▴ 10
0
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3
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1.2k
views
gene count in a GO term
affy affy
17.1 years ago Shi, Tao ▴ 720
0
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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 ▴ 360 • written 17.1 years ago by 25k
0
votes
1
reply
926
views
How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
affy affy
updated 17.1 years ago by 21k • written 17.1 years ago by ▴ 360
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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
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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
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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 21k • written 17.2 years ago by ▴ 270
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0
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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
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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…
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Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
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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".
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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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