Showing : hgu95av2 • reset
0
votes
5
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2.2k
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ReadAffy() Error - 2 Platforms in one file
hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hu6800 u133x3p hgu133a hgu133b hgu133plus2
updated 8.0 years ago by ▴ 110 • written 11.9 years ago by ▴ 760
0
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5
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2.5k
views
failing to filter ExpressionSet object using nsFilter
hgu95av2 hgu95av2
updated 9.8 years ago by 25k • written 9.8 years ago by ★ 13k
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0
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1.3k
views
GEOquery/virtualArray package error
Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray
10.0 years ago Guest User ★ 13k
0
votes
0
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1.5k
views
[phenoTest package]: gsea.kegg error with absVals parameter
Pathways GO hgu133a hgu95av2 phenoTest Pathways GO hgu133a hgu95av2 phenoTest
10.1 years ago Kostas Kerkentzes ▴ 10
0
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1
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1.6k
views
Non-specific filtering of Affymetrix Microarray data
GO hgu95av2 GO hgu95av2
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ★ 13k
2
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3
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1.1k
views
Creating Annotation package for GPL10427
Annotation hgu95av2 Annotation hgu95av2
updated 10.5 years ago by 65k • written 10.5 years ago by ★ 13k
0
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2
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3.2k
views
getGmt error
GO hgu95a hgu95av2 GO hgu95a hgu95av2
updated 10.6 years ago by 25k • written 10.6 years ago by ★ 13k
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0
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1.7k
views
library(\"geneplotter\") fails on load
GO hgu95av2 geneplotter GO hgu95av2 geneplotter
10.9 years ago Guest User ★ 13k
0
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6
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1.3k
views
serious problem with GOstats package
GO hgu95av2 GOstats GO hgu95av2 GOstats
updated 10.9 years ago by ★ 8.2k • written 11.0 years ago by ▴ 430
0
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1
reply
1.8k
views
nsfilter error from expressionset obtained after using aroma for processing
Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 810
0
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1
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2.0k
views
enrichment of GO terms based on input gene list
GO hgu95av2 GO hgu95av2
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ★ 13k
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2
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1.6k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 80
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1
reply
4.0k
views
getAnnMap: package hgu95av2 not available
hgu95av2 hgu95av2
updated 11.2 years ago by 25k • written 11.2 years ago by ★ 13k
0
votes
1
reply
992
views
Annotation databases--unable to get annotations
Annotation GO hgu95av2 probe limma Annotation GO hgu95av2 probe limma
updated 11.5 years ago by 65k • written 11.5 years ago by ★ 13k
0
votes
0
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935
views
gene2pathway retrain() error: species \'hsa\' unknown
Organism hgu95av2 gene2pathway Organism hgu95av2 gene2pathway
11.8 years ago Guest User ★ 13k
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0
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1.1k
views
Mapping genes to their gene sets for GSEA
Microarray Genetics GO hgu95av2 hgug4112a Microarray Genetics GO hgu95av2 hgug4112a
11.9 years ago Yoo, Seungyeul ▴ 110
0
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1
reply
3.5k
views
problems generating a gene2GOlist in topGO
Genetics Annotation GO hgu95av2 convert biomaRt topGO Genetics Annotation GO hgu95av2
updated 12.1 years ago by ▴ 400 • written 12.1 years ago by ▴ 490
0
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1
reply
1.3k
views
creating a UniprotIdentifier within GSEABase
Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase
updated 12.7 years ago by 25k • written 12.7 years ago by ▴ 910
0
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0
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863
views
Help with interpreting GEO derived data values
GO hgu95av2 GO hgu95av2
12.8 years ago Ochsner, Scott A ▴ 60
0
votes
1
reply
900
views
Use of createSimpleBimap
hgu95av2 AnnotationDbi hgu95av2 AnnotationDbi
updated 13.1 years ago by ★ 4.2k • written 13.1 years ago by ★ 1.1k
0
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13
replies
2.2k
views
Hypergeometric test with Disease Ontology
GO hgu95av2 GO hgu95av2
updated 13.2 years ago by ▴ 300 • written 13.2 years ago by ▴ 60
0
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0
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923
views
Problem in affypdnn package
hgu95av2 affypdnn hgu95av2 affypdnn
13.8 years ago Hasan, Ahmed Ryadh - hasar001 ▴ 20
0
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1
reply
1.2k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 930
0
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0
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1.0k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
13.9 years ago January Weiner ▴ 370
0
votes
1
reply
1.1k
views
filtering in GSEABase package
GO hgu95av2 mouse4302 PROcess Category GO hgu95av2 mouse4302 PROcess Category
updated 14.1 years ago by ▴ 610 • written 14.1 years ago by ▴ 190
0
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1
reply
1.5k
views
KEGGSOAP, hgu95av2.db: limited functionality
Pathways hgu95av2 probe KEGGSOAP Pathways hgu95av2 probe KEGGSOAP
updated 14.2 years ago by ★ 7.2k • written 14.2 years ago by ▴ 70
0
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1
reply
1.5k
views
CNV analysis with cghMCR/CNTools
GO CGH hgu133a hgu95av2 GO CGH hgu133a hgu95av2
updated 14.2 years ago by ★ 2.9k • written 14.2 years ago by ★ 1.1k
0
votes
1
reply
1.0k
views
extracting all GO terms from GOHyperGResult object?
Annotation GO hgu95av2 GOstats Annotation GO hgu95av2 GOstats
updated 14.2 years ago by ▴ 610 • written 14.2 years ago by ★ 2.0k
0
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0
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1.3k
views
mget() error with NA values
Microarray Annotation hgu133plus2 hgu95av2 AnnotationDbi Microarray Annotation hgu133plus2
15.0 years ago James W. MacDonald 65k
0
votes
0
replies
886
views
Bioconductor package to map probe set ids from one chip to another chip
Annotation GO Cancer hgu133a hgu95av2 probe Biostrings Annotation GO Cancer hgu133a
15.0 years ago Hervé Pagès 16k
0
votes
2
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4.8k
views
How to go from affymetrix to Ensembl transcript IDs
hgu95av2 affy biomaRt hgu95av2 affy biomaRt
updated 15.0 years ago by ★ 13k • written 15.0 years ago by ▴ 300
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0
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1.1k
views
browseGenome width question (rtracklayer)
Epigenetics GO hgu95av2 GLAD rtracklayer Epigenetics GO hgu95av2 GLAD rtracklayer
15.2 years ago Michael Lawrence ▴ 620
0
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1
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1.2k
views
GOstats: HyperGTest for KEGG
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
updated 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 180
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0
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1.1k
views
GOstats: hyperGTest for KEGG with org.Sc.sgd.db
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
15.3 years ago Paul Evans ▴ 180
0
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0
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1.2k
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sd==0 for some probesets when using gcrma
Microarray Proteomics Epigenetics Normalization GO Cancer hgu95av2 affy graph gcrma GO
15.4 years ago Dick Beyer ★ 1.4k
0
votes
7
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1.4k
views
Rkeys function from AnnotationDbi returns all Rkeys for a subset
hgu95av2 hgu95av2
updated 15.4 years ago by 65k • written 15.4 years ago by ▴ 110
0
votes
0
replies
820
views
hyperGTest on KEGG and PFAM with org.XX.eg annotations
Microarray Annotation Escherichia coli hgu95av2 Category Microarray Annotation hgu95av2
15.4 years ago Marc Carlson ★ 7.2k
0
votes
0
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994
views
hyperGTest on KEGG and PFAM with org.XX.eg annotations
Microarray Annotation Escherichia coli hgu95av2 Microarray Annotation Escherichia coli
15.4 years ago James F. Reid ▴ 610
0
votes
0
replies
880
views
Trouble Loading Rgraphviz in BioC 2.2 and 2.3
hgu95av2 Rgraphviz hgu95av2 Rgraphviz
15.4 years ago McGee, Monnie ▴ 300
0
votes
0
replies
945
views
Mean Plots and Heat Maps for Chromosome Bands
Pathways hgu95av2 Pathways hgu95av2
15.4 years ago McGee, Monnie ▴ 300
0
votes
1
reply
916
views
browseGenome width question (rtracklayer)
GO hgu95av2 GO hgu95av2
updated 15.4 years ago by ▴ 620 • written 15.4 years ago by ★ 1.1k
0
votes
8
replies
1.7k
views
Annotation packages
Annotation GO hgu95av2 affy limma Annotation GO hgu95av2 affy limma
updated 15.5 years ago by 21k • written 15.5 years ago by ▴ 350
0
votes
2
replies
945
views
hyperGTest
GO hgu133a hgu133plus2 hgu95av2 GO hgu133a hgu133plus2 hgu95av2
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ★ 1.2k
0
votes
3
replies
1.0k
views
Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0
GO hgu95av2 Biobase annotate GO hgu95av2 Biobase annotate
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 300
0
votes
1
reply
823
views
Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0
GO hgu95av2 Biobase annotate GO hgu95av2 Biobase annotate
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 300
0
votes
2
replies
1.2k
views
GeneR fail to compile
hgu95av2 GeneR hgu95av2 GeneR
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ▴ 120
0
votes
1
reply
853
views
How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
Cancer hgu95av2 affy Cancer hgu95av2 affy
updated 15.6 years ago by ▴ 360 • written 15.6 years ago by 25k
0
votes
3
replies
2.4k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
15.7 years ago anna freni sterrantino ▴ 120
0
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0
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1.2k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
15.7 years ago Chanchal Kumar ▴ 130
0
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1
reply
1.4k
views
GSEABase error in parsing msigdb_v2.5.xml
GO Infrastructure hgu95av2 Biobase Ruuid AnnotationDbi GO Infrastructure hgu95av2 Biobase
updated 15.9 years ago by 25k • written 15.9 years ago by ▴ 130
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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