Showing : annaffy • reset
0
votes
6
replies
1.4k
views
Many missing GO terms from GOHyperG call using mgu74av2
GO Survival hgu95av2 mgu74av2 Ruuid annotate multtest affy graph annaffy RBGL GOstats
updated 18.8 years ago by ★ 7.4k • written 18.8 years ago by ★ 1.4k
0
votes
4
replies
1.2k
views
rae230a/b data packages buggy?
Annotation rae230a rae230b affy annaffy Annotation rae230a rae230b affy annaffy
updated 20.7 years ago by ★ 2.9k • written 20.7 years ago by ▴ 110
0
votes
5
replies
5.0k
views
Affymetrix probeset ids to gene symbols
annaffy annaffy
updated 15.8 years ago by ▴ 160 • written 15.8 years ago by ▴ 300
0
votes
4
replies
984
views
Recent changes to Bioconductor packages
GO annaffy GO annaffy
20.0 years ago • updated 19.9 years ago madman@jimmy.harvard.edu ▴ 850
0
votes
4
replies
1.4k
views
coerce aafTable object into dataframe (annaffy)
annaffy annaffy
18.2 years ago • updated 18.1 years ago Georg Otto ▴ 510
0
votes
4
replies
960
views
GO package
annaffy annaffy
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ▴ 490
0
votes
3
replies
1.1k
views
Recent changes to Bioconductor packages
genefilter affy graph Rgraphviz limma annaffy genefilter affy graph Rgraphviz limma
20.6 years ago madman@jimmy.harvard.edu ▴ 850
0
votes
5
replies
2.6k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 9.8 years ago by ▴ 160 • written 9.9 years ago by 65k
0
votes
3
replies
1.0k
views
misnamed annotation environments with annaffy
Annotation annaffy Annotation annaffy
updated 18.9 years ago by ★ 7.4k • written 18.9 years ago by ▴ 320
0
votes
3
replies
1.1k
views
INstalling devel version
Microarray Pharmacogenomics Annotation GO Cancer cdf probe affy makecdfenv limma annaffy
19.7 years ago Mayte Suarez-Farinas ▴ 300
0
votes
9
replies
1.8k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ★ 2.2k
0
votes
3
replies
1.1k
views
latest devel GO package not built in R2.0.0
GO mouse4302 affy annaffy GO mouse4302 affy annaffy
updated 19.6 years ago by ★ 2.9k • written 19.6 years ago by ★ 1.4k
0
votes
3
replies
1.2k
views
Install of 1.5 Packages fails
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray
updated 19.5 years ago by ★ 5.5k • written 19.5 years ago by ★ 1.7k
0
votes
2
replies
1.5k
views
annaffy: YEAST vs. Affy YEAST_2 annotation
Annotation Yeast probe annaffy AnnBuilder Annotation Yeast probe annaffy AnnBuilder
updated 19.2 years ago by ▴ 220 • written 19.2 years ago by ▴ 320
0
votes
2
replies
1.1k
views
problem with annaffy aafFunction function
GO hgu95av2 rat2302 Biobase annotate reposTools affy annaffy GO hgu95av2 rat2302 affy
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 890
0
votes
2
replies
1.0k
views
2fold sigchanges from limma
GO Survival hgu133a2 annotate hexbin limma gcrma matchprobes annaffy GO Survival hexbin
updated 17.4 years ago by 50k • written 17.4 years ago by ▴ 60
0
votes
2
replies
1.6k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.1 years ago by 50k • written 17.1 years ago by ▴ 680
0
votes
2
replies
1.2k
views
getURL in annaffy fails when object length==1 (or how to cope with collapsed lists, arrays, etc?)
annaffy annaffy
updated 16.2 years ago by ▴ 540 • written 16.2 years ago by ▴ 30
0
votes
12
replies
2.0k
views
Building BioC 2.2 with R 2.7.0
GO annaffy simpleaffy GO annaffy simpleaffy
updated 15.9 years ago by ▴ 630 • written 15.9 years ago by ▴ 160
0
votes
7
replies
1.7k
views
Missing GeneSymbol and Name information in TopTable
Annotation hgu133plus2 annaffy affylmGUI Annotation hgu133plus2 annaffy affylmGUI
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ▴ 40
0
votes
3
replies
1.2k
views
annotation of affymetrix microarray data
annotate annaffy annotate annaffy
updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 90
0
votes
3
replies
1.4k
views
help with annaffy package
GO annaffy GO annaffy
13.9 years ago Taylor, Katie ▴ 90
0
votes
2
replies
1.2k
views
help with illumina microarray (DASL)
Microarray Annotation annaffy lumi Microarray Annotation annaffy lumi
updated 13.9 years ago by ★ 1.2k • written 13.9 years ago by ▴ 90
1
vote
10
replies
2.6k
views
Error installing Annaffy
affy annaffy go.db kegg.db
updated 7.0 years ago by 65k • written 7.0 years ago by • 0
0
votes
1
reply
1.2k
views
Warning message with dChip method
Annotation Normalization GO Cancer moe430a moe430b cdf affy limma gcrma annaffy PROcess
updated 20.1 years ago by ★ 2.3k • written 20.1 years ago by ▴ 210
0
votes
1
reply
986
views
annotation problem with hgu133plus2
Annotation GO hgu133plus2 cdf annotate affy siggenes annaffy Annotation GO hgu133plus2
18.9 years ago Yanqin Yang ▴ 250
0
votes
1
reply
1.4k
views
question about limma2annaffy
GO Survival Biobase annotate genefilter geneplotter affy affydata graph limma annaffy
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
0
votes
1
reply
1.5k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 10.3 years ago by 65k • written 10.3 years ago by ★ 13k
0
votes
1
reply
751
views
OMIM and annaffy
affy annaffy affy annaffy
updated 16.7 years ago by 65k • written 16.7 years ago by ▴ 510
3
votes
1
reply
1.1k
views
Gene Ontology link in aaf.handler() not working
annaffy aafTableAnn Gene Ontology aaf.handler()
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
0
votes
1
reply
930
views
help with multtest and annaffy
annaffy annaffy
updated 13.9 years ago by 65k • written 13.9 years ago by ▴ 90
0
votes
2
replies
1.2k
views
affycoretools vennSelect problem
GO Survival annotate genefilter affy graph gcrma annaffy RBGL GOstats biomaRt affyio
updated 15.8 years ago by 65k • written 15.8 years ago by ▴ 30
0
votes
1
reply
1.7k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 13.4 years ago by 25k • written 13.4 years ago by ▴ 20
0
votes
2
replies
4.0k
views
Human Gene 1.0 ST array
Annotation probe annaffy Annotation probe annaffy
updated 15.5 years ago by 65k • written 15.5 years ago by ▴ 10
0
votes
5
replies
1.2k
views
annotation information about ecoli2
Annotation GO probe annaffy Annotation GO probe annaffy
updated 15.5 years ago by 65k • written 15.5 years ago by ▴ 10
0
votes
1
reply
930
views
problem with the structure of a list of pathways
Genetics Pathways probe annaffy Genetics Pathways probe annaffy
updated 14.8 years ago by 65k • written 14.8 years ago by ▴ 60
0
votes
1
reply
897
views
Multiple genes per probeset
Annotation Cancer mouse4302 annaffy ASSIGN Annotation Cancer mouse4302 annaffy ASSIGN
updated 14.0 years ago by 65k • written 14.0 years ago by ★ 2.0k
0
votes
1
reply
895
views
GO problems with annaffy
GO hgu133a probe reposTools annaffy GO hgu133a probe reposTools annaffy
updated 20.0 years ago by ▴ 100 • written 20.0 years ago by ▴ 10
0
votes
1
reply
903
views
error in annaffy (multiget)
annaffy annaffy
updated 19.8 years ago by ▴ 220 • written 19.8 years ago by ▴ 300
0
votes
2
replies
1.0k
views
list of annaffy .db files?
Annotation annotate annaffy Annotation annotate annaffy
updated 13.6 years ago by 6.7k • written 13.6 years ago by ▴ 80
0
votes
2
replies
1.3k
views
probe to entrezID mapping with aafLocusLink
GO hgu133plus2 probe annaffy convert GO hgu133plus2 probe annaffy convert
updated 14.4 years ago by 65k • written 14.4 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 19.3 years ago by ★ 5.5k • written 19.3 years ago by ▴ 10
0
votes
1
reply
664
views
annaffy's annotation update
annaffy annaffy
updated 19.3 years ago by ★ 5.5k • written 19.3 years ago by ▴ 210
0
votes
1
reply
762
views
annaffy installation
annaffy annaffy
updated 20.3 years ago by ★ 3.9k • written 20.3 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Possible problem with Rhesus array annotation package
Annotation GO annotate annaffy Annotation GO annotate annaffy
updated 12.8 years ago by ★ 7.2k • written 12.8 years ago by ▴ 30
0
votes
1
reply
883
views
rbind in annaffy problem
GO hgu95av2 rat2302 cdf annotate affy graph annaffy RBGL GOstats biomaRt GO hgu95av2
updated 18.4 years ago by 65k • written 18.4 years ago by ▴ 890
0
votes
1
reply
1.1k
views
New Package: annaffy
Annotation GO rgu34a probe Biobase annaffy Annotation GO rgu34a probe Biobase annaffy
updated 21.7 years ago by ★ 2.3k • written 21.7 years ago by ▴ 20
0
votes
2
replies
1.1k
views
AnnBuilder problem for mu11ksuba
Organism mu11ksuba annotate limma gcrma matchprobes annaffy AnnBuilder Organism mu11ksuba
updated 18.1 years ago by ▴ 780 • written 18.1 years ago by ★ 1.4k
0
votes
1
reply
873
views
Annaffy problem loading metadata
mouse4302 annaffy mouse4302 annaffy
17.9 years ago Bornman, Daniel M ▴ 110
0
votes
1
reply
752
views
error in annaffy
annaffy annaffy
updated 17.0 years ago by 65k • written 17.0 years ago by ▴ 510
50 results • Page 1 of 1
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Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
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In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
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Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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