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Showing :
affycoretools
•
reset
0
votes
4
replies
4.2k
views
Extracting genes within venn diagram
limma
affycoretools
limma
affycoretools
15.5 years ago
Celine Carret
▴ 220
0
votes
3
replies
4.0k
views
PCA-prcomp() versus plotPCA
affycoretools
affycoretools
updated 17.5 years ago by
James W. MacDonald
65k • written 17.5 years ago by
marco fabbri
▴ 320
9
votes
6
replies
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 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
svlachavas
▴ 830
6
votes
7
replies
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
Yang Shi
▴ 10 • written 7.1 years ago by
svlachavas
▴ 830
0
votes
4
replies
2.9k
views
Error: could not find function "plotPCA"
GO
affycoretools
KEGGREST
GO
affycoretools
KEGGREST
updated 10.0 years ago by
Michael Love
41k • written 10.0 years ago by
Surles, Monique
▴ 50
2
votes
4
replies
2.2k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools
clariom
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
willj
▴ 30
0
votes
3
replies
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
James W. MacDonald
65k • written 11.1 years ago by
Jenny Drnevich
★ 2.0k
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
James W. MacDonald
65k • written 17.1 years ago by
Jenny Drnevich
★ 2.2k
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
James W. MacDonald
65k • written 15.6 years ago by
Manisha Brahmachary
▴ 80
0
votes
10
replies
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
Jenny Drnevich
★ 2.2k • written 16.6 years ago by
Seth Falcon
★ 7.4k
0
votes
3
replies
1.7k
views
affycoretools::annotateEset unable to find inherited method
affycoretools
missing file link
annotateEset
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
willie.yu.ncc
• 0
0
votes
3
replies
1.6k
views
Help in installing affycoretools
affycoretools
affycoretools
updated 14.5 years ago by
Martin Morgan
25k • written 14.5 years ago by
Sunny Srivastava
▴ 350
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
3
replies
1.6k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools
FRMA
affyio
AffymetrixDataTestFiles
affy
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Seymoo
• 0
0
votes
5
replies
1.5k
views
error coercing an exprSet to ExpressionSet
GO
cdf
Biobase
annotate
multtest
affy
limma
RBGL
GOstats
Category
affycoretools
GO
cdf
updated 17.5 years ago by
Seth Falcon
★ 7.4k • written 17.5 years ago by
Kimpel, Mark W
▴ 890
0
votes
6
replies
1.5k
views
RNA degradation tends & options for analysis
affy
limma
gcrma
affycoretools
affy
limma
gcrma
affycoretools
updated 18.2 years ago by
James W. MacDonald
65k • written 18.2 years ago by
Juanma Vaquerizas
▴ 20
0
votes
7
replies
1.5k
views
vennSelect error
GO
hgu133a2
yeast2
affy
affycoretools
GO
hgu133a2
yeast2
affy
affycoretools
updated 12.9 years ago by
James W. MacDonald
65k • written 12.9 years ago by
mali salmon
▴ 370
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
James W. MacDonald
65k • written 6.7 years ago by
relathman
▴ 20
0
votes
3
replies
1.4k
views
affycoretools repost
GO
limma
affycoretools
GO
limma
affycoretools
updated 15.9 years ago by
James W. MacDonald
65k • written 15.9 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
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
James W. MacDonald
65k • written 4.8 years ago by
Guido Hooiveld
★ 3.9k
0
votes
0
replies
1.4k
views
identifying drosophila miRNA targets
miRNA
drosophila2
probe
affy
convert
affycoretools
microRNA
miRNA
drosophila2
probe
affy
11.1 years ago
Fiona
▴ 70
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
bastien_chassagnol
• 0
3
votes
5
replies
1.4k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.3k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
Jenny Drnevich
★ 2.0k
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
3
votes
5
replies
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
James W. MacDonald
65k • written 4.4 years ago by
giroudpaul
▴ 40
0
votes
2
replies
1.3k
views
oligo package - aggregate transcript expression to gene
affycoretools
oligo
3.5 years ago
Luca
• 0
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
James W. MacDonald
65k • written 6.2 years ago by
biostR
▴ 10
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
James W. MacDonald
65k • written 6.3 years ago by
eleonoregravier
▴ 70
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 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
svlachavas
▴ 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
James W. MacDonald
65k • written 4.1 years ago by
svlachavas
▴ 830
0
votes
3
replies
1.2k
views
intended behavior of plotPCA and AffyBatch objects?
affy
affycoretools
affy
affycoretools
updated 17.0 years ago by
James W. MacDonald
65k • written 17.0 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
1.2k
views
affycoretools question
GO
limma
affycoretools
GO
limma
affycoretools
updated 15.9 years ago by
James W. MacDonald
65k • written 15.9 years ago by
Louisa A Rispoli/AS/EXP/UTIA
▴ 160
0
votes
1
reply
1.1k
views
why kOverA function has 6
affycoretools
affycoretools
updated 13.0 years ago by
Gang Chen
▴ 20 • written 13.0 years ago by
wang peter
★ 2.0k
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
1
vote
1
reply
1.1k
views
affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Gerhard Thallinger
▴ 180
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
14.9 years ago
James W. MacDonald
65k
0
votes
2
replies
1.1k
views
justRMA using incorrect default cdf
GO
Survival
rat2302
cdf
annotate
genefilter
affy
limma
affycoretools
GO
Survival
cdf
18.3 years ago
Kimpel, Mark W
▴ 890
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
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
James W. MacDonald
65k • written 13.2 years ago by
Assa Yeroslaviz
★ 1.5k
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
1
reply
917
views
affycoretools limma2annaffy fold change output question
affycoretools
affycoretools
updated 18.1 years ago by
James W. MacDonald
65k • written 18.1 years ago by
Kimpel, Mark W
▴ 890
0
votes
1
reply
777
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
James W. MacDonald
65k • written 17.2 years ago by
Mark W Kimpel
▴ 830
1
vote
1
reply
760
views
afffycoretools - warnings in mirna2mrna()
affycoretools
DBI
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Gerhard Thallinger
▴ 180
1
vote
1
reply
736
views
affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
affycoretools
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Gerhard Thallinger
▴ 180
47 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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