Showing : affycoretools • reset
0
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407
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Custom CDF creation for HTA 2.0 array using GTF annotation
oligo oligoClasses pdInfoBuilder affycoretools affyio
6 months ago Seymoo • 0
0
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3
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3.6k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
1
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1
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1.1k
views
affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
affycoretools
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 180
1
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1
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1.6k
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affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 180
1
vote
1
reply
1.1k
views
afffycoretools - warnings in mirna2mrna()
affycoretools DBI
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 180
0
votes
3
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2.0k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 4.8 years ago by 68k • written 4.9 years ago by • 0
0
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2
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1.7k
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
5.0 years ago Luca • 0
5
votes
5
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1.8k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 840
3
votes
5
replies
2.0k
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 40
1
vote
2
replies
1.9k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 6.3 years ago by 68k • written 6.3 years ago by ★ 4.1k
1
vote
5
replies
1.8k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 840
0
votes
3
replies
2.1k
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
2
votes
4
replies
1.7k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 10
1
vote
3
replies
1.7k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 70
2
votes
4
replies
2.8k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 30
2
votes
3
replies
1.9k
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 8.2 years ago by 68k • written 8.2 years ago by ▴ 20
6
votes
7
replies
4.0k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 3.4 years ago by ▴ 10 • written 8.6 years ago by ▴ 840
9
votes
6
replies
4.5k
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 8.7 years ago by 68k • written 8.7 years ago by ▴ 840
0
votes
3
replies
1.7k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 8.7 years ago by 68k • written 8.7 years ago by ★ 2.0k
3
votes
5
replies
1.8k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 10.5 years ago by 68k • written 10.5 years ago by ★ 2.0k
0
votes
4
replies
3.5k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 11.4 years ago by 43k • written 11.4 years ago by ▴ 50
0
votes
3
replies
2.3k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 12.6 years ago by 68k • written 12.6 years ago by ★ 2.0k
0
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0
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1.7k
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
12.6 years ago Fiona ▴ 70
0
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7
replies
2.0k
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 14.4 years ago by 68k • written 14.4 years ago by ▴ 370
0
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1
reply
1.4k
views
why kOverA function has 6
affycoretools affycoretools
updated 14.5 years ago by ▴ 20 • written 14.5 years ago by ★ 2.0k
0
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0
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1.4k
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
14.7 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.3k
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 14.7 years ago by 68k • written 14.7 years ago by ★ 1.5k
0
votes
3
replies
2.0k
views
Help in installing affycoretools
affycoretools affycoretools
updated 15.9 years ago by 25k • written 15.9 years ago by ▴ 350
0
votes
0
replies
1.4k
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
16.3 years ago James W. MacDonald 68k
0
votes
4
replies
4.9k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
17.0 years ago Celine Carret ▴ 220
0
votes
0
replies
1.3k
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
17.1 years ago James W. MacDonald 68k
0
votes
2
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2.0k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 17.1 years ago by 68k • written 17.1 years ago by ▴ 80
0
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0
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1.3k
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
17.1 years ago rgentleman ★ 5.5k
0
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3
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1.7k
views
affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 17.3 years ago by 68k • written 17.3 years ago by ▴ 160
0
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1
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1.4k
views
affycoretools question
GO limma affycoretools GO limma affycoretools
updated 17.4 years ago by 68k • written 17.4 years ago by ▴ 160
0
votes
10
replies
2.3k
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 18.1 years ago by ★ 2.2k • written 18.1 years ago by ★ 7.4k
0
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3
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1.6k
views
intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 18.5 years ago by 68k • written 18.5 years ago by ★ 2.2k
0
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3
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2.3k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 18.6 years ago by 68k • written 18.6 years ago by ★ 2.2k
0
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2
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2.0k
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
18.7 years ago Mark W Kimpel ▴ 830
0
votes
1
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1.1k
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 18.7 years ago by 68k • written 18.7 years ago by ▴ 830
0
votes
5
replies
2.2k
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ▴ 890
0
votes
0
replies
1.3k
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
19.0 years ago Kimpel, Mark W ▴ 890
0
votes
3
replies
4.7k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 19.0 years ago by 68k • written 19.0 years ago by ▴ 320
0
votes
0
replies
1.4k
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
19.0 years ago James W. MacDonald 68k
0
votes
2
replies
1.7k
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
19.4 years ago Kimpel, Mark W ▴ 890
0
votes
1
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1.1k
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 19.5 years ago by 68k • written 19.5 years ago by ▴ 890
0
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6
replies
2.0k
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 19.7 years ago by 68k • written 19.7 years ago by ▴ 20
0
votes
2
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1.3k
views
justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
19.7 years ago Kimpel, Mark W ▴ 890
48 results • Page 1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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