Showing : Category • reset
0
votes
12
replies
3.2k
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 19.0 years ago by ★ 7.4k • written 19.0 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 17.4 years ago by ★ 7.4k • written 17.4 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
2.0k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by ▴ 930
0
votes
2
replies
985
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 16.6 years ago by ▴ 500 • written 16.6 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 8.0 years ago by ▴ 10 • written 12.6 years ago by ▴ 10
0
votes
3
replies
1.3k
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 14.3 years ago by ▴ 70 • written 14.3 years ago by ▴ 60
0
votes
3
replies
955
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 19.7 years ago by ★ 1.8k • written 19.7 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 16.9 years ago by ★ 7.4k • written 16.9 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
932
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
895
views
GO.db redundance
Annotation GO probe Category Annotation GO probe Category
updated 14.9 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 15.4 years ago by ▴ 90 • written 15.4 years ago by ▴ 830
0
votes
4
replies
1.9k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by 50k
0
votes
1
reply
953
views
Limma and Genepix
limma Category limma Category
updated 18.9 years ago by 50k • written 18.9 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 12.6 years ago by ★ 3.9k • written 12.6 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 20.4 years ago by ▴ 70 • written 20.4 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
951
views
Affy mas5calls on Hu6800 arrays
Cancer hu6800 probe affy Category Cancer hu6800 probe affy Category
19.5 years ago • updated 19.4 years ago Stronach, Euan A ▴ 20
0
votes
1
reply
933
views
warnings or potential problems in limma procedure
limma Category limma Category
13.0 years ago Yi, Ming NIH/NCI [C] ▴ 100
0
votes
1
reply
807
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
727
views
GoHyperG question
GO GOstats Category GO GOstats Category
updated 19.7 years ago by ★ 2.9k • written 19.7 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
814
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 16.1 years ago by ▴ 570 • written 16.1 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 17.2 years ago by 65k • written 17.2 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 19.7 years ago by ★ 1.8k • written 19.7 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
791
views
GO Term2entrezgene
Category Category
updated 15.5 years ago by 21k • written 15.5 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
860
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 17.3 years ago by 65k • written 17.3 years ago by ▴ 890
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Scholar to Robert Castelo ★ 3.2k
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