Showing : affycoretools • reset
0
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10
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1.7k
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 16.6 years ago by ★ 2.2k • written 16.6 years ago by ★ 7.4k
0
votes
7
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1.5k
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 12.9 years ago by 65k • written 12.9 years ago by ▴ 370
6
votes
7
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3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 23 months ago by ▴ 10 • written 7.1 years ago by ▴ 830
9
votes
6
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3.9k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 830
0
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6
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1.5k
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 18.2 years ago by 65k • written 18.2 years ago by ▴ 20
3
votes
5
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1.3k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 9.0 years ago by 65k • written 9.0 years ago by ★ 2.0k
3
votes
5
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1.3k
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 40
0
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5
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1.5k
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 890
1
vote
5
replies
1.2k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 830
5
votes
5
replies
1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
2
votes
4
replies
2.2k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 6.6 years ago by 65k • written 6.6 years ago by ▴ 30
0
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4
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4.2k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
15.5 years ago Celine Carret ▴ 220
2
votes
4
replies
1.3k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 10
0
votes
4
replies
2.9k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 9.9 years ago by 41k • written 9.9 years ago by ▴ 50
0
votes
3
replies
1.2k
views
intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 17.0 years ago by 65k • written 17.0 years ago by ★ 2.2k
0
votes
3
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1.3k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 7.2 years ago by 65k • written 7.2 years ago by ★ 2.0k
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 3.3 years ago by 65k • written 3.4 years ago by • 0
0
votes
3
replies
1.4k
views
affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 15.8 years ago by 65k • written 15.8 years ago by ▴ 160
0
votes
3
replies
4.0k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 17.5 years ago by 65k • written 17.5 years ago by ▴ 320
0
votes
3
replies
1.5k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
3
replies
1.8k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
0
votes
3
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2.0k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 11.1 years ago by 65k • written 11.1 years ago by ★ 2.0k
0
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3
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1.7k
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
1
vote
3
replies
1.2k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 6.3 years ago by 65k • written 6.3 years ago by ▴ 70
0
votes
3
replies
1.6k
views
Help in installing affycoretools
affycoretools affycoretools
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 350
2
votes
3
replies
1.5k
views
Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
pd.hta.2.0 hta2.0 affycoretools
updated 6.7 years ago by 65k • written 6.7 years ago by ▴ 20
0
votes
2
replies
1.3k
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
17.9 years ago Kimpel, Mark W ▴ 890
0
votes
2
replies
1.0k
views
justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
18.2 years ago Kimpel, Mark W ▴ 890
0
votes
2
replies
1.6k
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO Survival Biobase genefilter affy limma RBGL GOstats Category affyio affycoretools GO
17.2 years ago Mark W Kimpel ▴ 830
0
votes
2
replies
1.7k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 15.6 years ago by 65k • written 15.6 years ago by ▴ 80
1
vote
2
replies
1.4k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 4.8 years ago by 65k • written 4.8 years ago by ★ 3.9k
0
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2
replies
1.3k
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
3.5 years ago Luca • 0
0
votes
1
reply
772
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 17.2 years ago by 65k • written 17.2 years ago by ▴ 830
0
votes
1
reply
1.0k
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 13.2 years ago by 65k • written 13.2 years ago by ★ 1.5k
0
votes
1
reply
910
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 18.0 years ago by 65k • written 18.0 years ago by ▴ 890
1
vote
1
reply
752
views
afffycoretools - warnings in mirna2mrna()
affycoretools DBI
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 180
1
vote
1
reply
1.1k
views
affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 180
1
vote
1
reply
729
views
affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
affycoretools
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 180
0
votes
1
reply
1.1k
views
why kOverA function has 6
affycoretools affycoretools
updated 13.0 years ago by ▴ 20 • written 13.0 years ago by ★ 2.0k
0
votes
1
reply
1.2k
views
affycoretools question
GO limma affycoretools GO limma affycoretools
updated 15.8 years ago by 65k • written 15.8 years ago by ▴ 160
0
votes
0
replies
1.0k
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
17.5 years ago Kimpel, Mark W ▴ 890
0
votes
0
replies
1.1k
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
14.8 years ago James W. MacDonald 65k
0
votes
0
replies
1.0k
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
15.6 years ago James W. MacDonald 65k
0
votes
0
replies
1.0k
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
15.6 years ago rgentleman ★ 5.5k
0
votes
0
replies
1.1k
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
13.2 years ago Assa Yeroslaviz ★ 1.5k
0
votes
0
replies
1.1k
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
17.5 years ago James W. MacDonald 65k
0
votes
0
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1.4k
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
11.1 years ago Fiona ▴ 70
47 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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