Showing : affycoretools • reset
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Custom CDF creation for HTA 2.0 array using GTF annotation
oligo oligoClasses pdInfoBuilder affycoretools affyio
16 days ago • updated 15 days ago Seymoo • 0
0
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3
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3.1k
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*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
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1
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1.0k
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affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
affycoretools
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 180
1
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1.5k
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affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 180
1
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1
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979
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afffycoretools - warnings in mirna2mrna()
affycoretools DBI
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 180
0
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3
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1.8k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 4.3 years ago by 68k • written 4.4 years ago by • 0
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2
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1.6k
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oligo package - aggregate transcript expression to gene
affycoretools oligo
4.5 years ago Luca • 0
5
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5
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1.7k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 840
3
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5
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1.8k
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 40
1
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2
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1.8k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 5.8 years ago by 68k • written 5.8 years ago by ★ 4.1k
1
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5
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1.6k
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 840
0
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3
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2.0k
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
2
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4
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1.6k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 10
1
vote
3
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1.5k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 70
2
votes
4
replies
2.7k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 30
2
votes
3
replies
1.8k
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 7.7 years ago by 68k • written 7.7 years ago by ▴ 20
6
votes
7
replies
3.8k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 2.9 years ago by ▴ 10 • written 8.1 years ago by ▴ 840
9
votes
6
replies
4.4k
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 8.2 years ago by 68k • written 8.2 years ago by ▴ 840
0
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3
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1.6k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 8.2 years ago by 68k • written 8.2 years ago by ★ 2.0k
3
votes
5
replies
1.6k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 10.0 years ago by 68k • written 10.0 years ago by ★ 2.0k
0
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4
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3.3k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 50
0
votes
3
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2.2k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 12.1 years ago by 68k • written 12.1 years ago by ★ 2.0k
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0
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1.6k
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
12.1 years ago Fiona ▴ 70
0
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7
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1.8k
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 13.9 years ago by 68k • written 13.9 years ago by ▴ 370
0
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1
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1.3k
views
why kOverA function has 6
affycoretools affycoretools
updated 14.0 years ago by ▴ 20 • written 14.0 years ago by ★ 2.0k
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0
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1.3k
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
14.2 years ago Assa Yeroslaviz ★ 1.5k
0
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1.2k
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quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 14.2 years ago by 68k • written 14.2 years ago by ★ 1.5k
0
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3
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1.9k
views
Help in installing affycoretools
affycoretools affycoretools
updated 15.4 years ago by 25k • written 15.4 years ago by ▴ 350
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0
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1.3k
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
15.8 years ago James W. MacDonald 68k
0
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4
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4.8k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
16.5 years ago Celine Carret ▴ 220
0
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0
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1.2k
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
16.6 years ago James W. MacDonald 68k
0
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2
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1.9k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 16.6 years ago by 68k • written 16.6 years ago by ▴ 80
0
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0
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1.2k
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
16.6 years ago rgentleman ★ 5.5k
0
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3
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1.7k
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affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 16.8 years ago by 68k • written 16.8 years ago by ▴ 160
0
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1
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1.3k
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affycoretools question
GO limma affycoretools GO limma affycoretools
updated 16.8 years ago by 68k • written 16.8 years ago by ▴ 160
0
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10
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2.1k
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 17.6 years ago by ★ 2.2k • written 17.6 years ago by ★ 7.4k
0
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3
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1.5k
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intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 18.0 years ago by 68k • written 18.0 years ago by ★ 2.2k
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3
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2.1k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 18.1 years ago by 68k • written 18.1 years ago by ★ 2.2k
0
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2
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1.8k
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
18.2 years ago Mark W Kimpel ▴ 830
0
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1
reply
982
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 18.2 years ago by 68k • written 18.2 years ago by ▴ 830
0
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5
replies
2.0k
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ▴ 890
0
votes
0
replies
1.2k
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
18.5 years ago Kimpel, Mark W ▴ 890
0
votes
3
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4.6k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 18.5 years ago by 68k • written 18.5 years ago by ▴ 320
0
votes
0
replies
1.3k
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
18.5 years ago James W. MacDonald 68k
0
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2
replies
1.6k
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
18.9 years ago Kimpel, Mark W ▴ 890
0
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1
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1.1k
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 19.0 years ago by 68k • written 19.0 years ago by ▴ 890
0
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6
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1.9k
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 20
0
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2
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1.3k
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justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
19.2 years ago Kimpel, Mark W ▴ 890
48 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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