Showing : category • reset
0
votes
12
replies
3.3k
views
testing GO categories with Fisher's exact test.
GO Category GO Category
updated 20.2 years ago by 65k • written 20.2 years ago by ▴ 430
0
votes
11
replies
1.7k
views
'recursive default argument' error in GOENTREZID2GO
GO Biobase genefilter graph Category GO Biobase genefilter graph Category
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 260
0
votes
6
replies
1.4k
views
hyperGTest
GO Cancer GOstats Category GO Cancer GOstats Category
updated 17.0 years ago by ★ 6.0k • written 17.0 years ago by ★ 7.4k
0
votes
6
replies
1.2k
views
where to start?
Classification Clustering Category Classification Clustering Category
updated 19.1 years ago by ★ 7.4k • written 19.1 years ago by ▴ 40
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 ★ 7.4k • written 17.5 years ago by ▴ 890
0
votes
9
replies
2.3k
views
GSEA, topGO, GOstats...? what's a good way to look at GO over-representation?
affy Category nudge affy Category nudge
updated 14.2 years ago by ★ 13k • written 14.2 years ago by ★ 1.9k
0
votes
8
replies
2.1k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by ▴ 930
0
votes
2
replies
993
views
stat/math question on Category vignette
Pathways Category Pathways Category
updated 16.7 years ago by ★ 7.4k • written 16.7 years ago by ▴ 890
0
votes
4
replies
2.1k
views
disagreement between biomaRt and topGO
GO hgu133plus2 annotate geneplotter graph Rgraphviz PROcess goTools biomaRt Category GO
updated 16.7 years ago by ▴ 500 • written 16.7 years ago by ★ 1.4k
0
votes
4
replies
5.0k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO Category goseq GO Category goseq
updated 8.1 years ago by ▴ 10 • written 12.7 years ago by ▴ 10
0
votes
3
replies
1.4k
views
help with using Category package with makecdfenv built Gene ST package
GO cdf affy limma Category GO cdf affy limma Category
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ▴ 830
0
votes
2
replies
1.6k
views
Bioconductor Digest, Vol 82, Issue 20
Annotation Pathways affy GOstats Category AnnotationDbi Annotation Pathways affy GOstats
updated 14.4 years ago by ▴ 70 • written 14.4 years ago by ▴ 60
0
votes
3
replies
963
views
Trouble using GOstats
GO hgu133a Category GO hgu133a Category
updated 19.1 years ago by ★ 5.5k • written 19.1 years ago by ▴ 80
0
votes
3
replies
1.3k
views
grep GOID, R problem or my problem?
GO affy Category GO affy Category
updated 18.5 years ago by ★ 7.4k • written 18.5 years ago by ▴ 810
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
1.1k
views
hyperGTest and HyperGParams
Microarray Annotation GLAD Category Microarray Annotation GLAD Category
updated 16.5 years ago by ★ 5.5k • written 16.5 years ago by ▴ 500
0
votes
2
replies
1.0k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 190
0
votes
7
replies
1.4k
views
no summary of GOHyperGResult
GO GOstats Category GO GOstats Category
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 280
0
votes
2
replies
1.3k
views
KNN, SVM, and randomForest - How to predict test without known categories
Category Category
updated 19.8 years ago by ★ 1.8k • written 19.8 years ago by ▴ 120
0
votes
3
replies
1.9k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe limma Category probe limma Category
updated 12.1 years ago by 65k • written 12.1 years ago by ▴ 10
0
votes
2
replies
1.6k
views
function error for "hyperGTest" in Category package
Annotation probe Category Annotation probe Category
updated 14.5 years ago by 6.7k • written 14.5 years ago by ▴ 60
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 17.0 years ago by ★ 7.4k • written 17.0 years ago by ★ 2.2k
0
votes
5
replies
1.3k
views
retrieve genes names after KEGG hypergeometric test
Annotation Pathways GO rat2302 probe affy Category Annotation Pathways GO rat2302 probe
updated 13.5 years ago by ▴ 930 • written 13.5 years ago by ▴ 230
0
votes
5
replies
1.5k
views
problem with Category package and custom annotationDbi
Annotation Category AnnotationDbi Annotation Category AnnotationDbi
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ▴ 830
0
votes
4
replies
943
views
cateGOry error
GO Category GO Category
updated 16.9 years ago by ★ 13k • written 16.9 years ago by ▴ 260
0
votes
2
replies
905
views
GO.db redundance
Annotation GO probe Category Annotation GO probe Category
updated 15.0 years ago by ★ 7.2k • written 15.0 years ago by ▴ 40
0
votes
2
replies
1.1k
views
decideTests limitation to certain lfc and p values not working
Category beadarray Category beadarray
updated 13.5 years ago by ▴ 650 • written 13.5 years ago by ▴ 100
0
votes
2
replies
1.2k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 15.5 years ago by ▴ 90 • written 15.5 years ago by ▴ 830
0
votes
4
replies
2.0k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 12.6 years ago by ▴ 30 • written 12.6 years ago by 50k
0
votes
1
reply
959
views
Limma and Genepix
limma Category limma Category
updated 19.0 years ago by 50k • written 19.0 years ago by ▴ 40
0
votes
4
replies
1.6k
views
R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Breast Prostate probe Category xps Annotation Normalization xps
updated 12.7 years ago by ★ 3.9k • written 12.7 years ago by ▴ 80
0
votes
1
reply
1.1k
views
Annotating yeast ORFs with GO and KEGG
GO Yeast annotate Category GO Yeast annotate Category
updated 20.5 years ago by ▴ 70 • written 20.5 years ago by ▴ 80
0
votes
9
replies
1.2k
views
Help with 'annotation' in GOHyeprGParamsClass
Annotation GO Yeast Category Annotation GO Yeast Category
updated 15.5 years ago by ★ 5.5k • written 15.5 years ago by ▴ 50
0
votes
4
replies
1.4k
views
Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
Annotation GO annotate affy PROcess Category cycle Annotation GO annotate affy PROcess
updated 19.2 years ago by ▴ 310 • written 19.2 years ago by ▴ 250
0
votes
1
reply
957
views
Affy mas5calls on Hu6800 arrays
Cancer hu6800 probe affy Category Cancer hu6800 probe affy Category
19.5 years ago Stronach, Euan A ▴ 20
0
votes
1
reply
939
views
warnings or potential problems in limma procedure
limma Category limma Category
13.1 years ago Yi, Ming NIH/NCI [C] ▴ 100
0
votes
1
reply
813
views
how to exrtact col. names from exprs()
GO Category GO Category
updated 19.7 years ago by ★ 1.8k • written 19.7 years ago by ▴ 320
0
votes
1
reply
733
views
GoHyperG question
GO GOstats Category GO GOstats Category
updated 19.8 years ago by ★ 2.9k • written 19.8 years ago by ▴ 10
0
votes
1
reply
1.7k
views
problem with AnnotationDbi
ChipName db0 affy Category AnnotationDbi ChipName db0 affy Category AnnotationDbi
updated 15.5 years ago by 16k • written 15.5 years ago by ▴ 830
0
votes
1
reply
822
views
Combining old Affy arrays for limma
rat2302 rgu34a rgu34b rgu34c affy limma Category rat2302 rgu34a rgu34b rgu34c affy
updated 15.5 years ago by 21k • written 15.5 years ago by ▴ 300
0
votes
1
reply
1.2k
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category Category
updated 11.1 years ago by ▴ 60 • written 11.1 years ago by ▴ 30
0
votes
7
replies
1.3k
views
Odds Ratio in GOstat [resolved?]
GOstats Category GOstats Category
updated 17.4 years ago by ★ 6.0k • written 17.4 years ago by ★ 7.4k
0
votes
6
replies
2.2k
views
problem with GOHyperGParams in package Category
Annotation GO GOstats Category Annotation GO GOstats Category
updated 16.2 years ago by ▴ 570 • written 16.2 years ago by ▴ 830
0
votes
1
reply
1.1k
views
Problem with limma2biomaRt and MBNI custom CDF
Annotation GO cdf DynDoc genefilter tkWidgets affy graph limma RBGL biomaRt Category
updated 17.3 years ago by 65k • written 17.3 years ago by ▴ 300
0
votes
1
reply
1.6k
views
KNN, SVM, and randomForest - How to predict testing set without known categories (affy data)
Microarray Clustering Category Microarray Clustering Category
updated 19.8 years ago by ★ 1.8k • written 19.8 years ago by ▴ 120
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
1
reply
797
views
GO Term2entrezgene
Category Category
updated 15.6 years ago by 21k • written 15.6 years ago by ★ 1.2k
0
votes
6
replies
1.6k
views
GOstats and custom annotation problem
Annotation GO annotate genefilter graph AnnBuilder RBGL GOstats Category Annotation GO
updated 17.3 years ago by 21k • written 17.3 years ago by ▴ 310
0
votes
2
replies
865
views
dye effects stronger than dye-swaps?
Microarray Normalization Category Microarray Normalization Category
updated 17.0 years ago by ★ 6.0k • written 17.0 years ago by ★ 2.2k
0
votes
2
replies
1.6k
views
problem with hist.default in affystart in package affycoretools
GO cdf annotate affy limma RBGL simpleaffy GOstats Category affyQCReport affyio GO cdf
updated 17.4 years ago by 65k • written 17.4 years ago by ▴ 890
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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