Showing : category • reset
0
votes
4
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2.0k
views
R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Breast Prostate probe Category xps Annotation Normalization xps
updated 14.1 years ago by ★ 3.9k • written 14.1 years ago by ▴ 80
0
votes
0
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1.2k
views
goseq - overrepresented p-values (Alicia Oshlack)
GO Category goseq GO Category goseq
14.2 years ago Gu Mi ▴ 30
0
votes
1
reply
4.3k
views
goseq - overrepresented p-values
GO Category goseq GO Category goseq
updated 14.2 years ago by ▴ 100 • written 14.2 years ago by ▴ 30
0
votes
0
replies
858
views
colors in plotCtCategory heatmap
Category HTqPCR Category HTqPCR
14.3 years ago Heidi Dvinge ★ 2.0k
0
votes
0
replies
1.1k
views
question about mt.maxT output (multtest)
Sequencing Microarray Category Sequencing Microarray Category
14.3 years ago Les Dethlefsen ▴ 20
0
votes
0
replies
1.2k
views
question/issue with multtest mt.maxT
Sequencing Microarray GUI Category Sequencing Microarray GUI Category
14.3 years ago Les Dethlefsen ▴ 20
0
votes
1
reply
1.6k
views
how to do paired t-tests for multiple subgroups [was: warnings or potential problems in limma procedure]
Cancer limma GLAD Category Cancer limma GLAD Category
updated 14.4 years ago by ▴ 100 • written 14.4 years ago by 53k
0
votes
1
reply
1.5k
views
warnings or potential problems in limma procedure
Cancer limma Category Cancer limma Category
updated 14.4 years ago by ▴ 100 • written 14.4 years ago by 53k
0
votes
1
reply
1.2k
views
warnings or potential problems in limma procedure
limma Category limma Category
14.4 years ago Yi, Ming NIH/NCI [C] ▴ 100
0
votes
1
reply
3.1k
views
goseq KEGG testing?
Pathways GO PROcess Category goseq Pathways GO PROcess Category goseq
updated 14.5 years ago by ▴ 40 • written 14.5 years ago by ★ 2.0k
0
votes
1
reply
2.4k
views
Can I know the number of genes in enriched GO category using GOseq
GO annotate Category goseq GO annotate Category goseq
updated 14.5 years ago by ▴ 40 • written 14.6 years ago by ▴ 150
0
votes
4
replies
2.2k
views
Category R CMD check and not reloading required packages
Category Category
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 280
0
votes
1
reply
3.0k
views
limma topTable annotation
GO hgu133plus2 affy limma convert Category GO hgu133plus2 affy limma convert Category
updated 14.6 years ago by ▴ 130 • written 14.6 years ago by 53k
0
votes
2
replies
2.1k
views
problem extending Category classes
Annotation GO Category Annotation GO Category
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 280
0
votes
2
replies
1.4k
views
decideTests limitation to certain lfc and p values not working
Category beadarray Category beadarray
updated 14.9 years ago by ▴ 650 • written 14.9 years ago by ▴ 100
0
votes
5
replies
1.7k
views
retrieve genes names after KEGG hypergeometric test
Annotation Pathways GO rat2302 probe affy Category Annotation Pathways GO rat2302 probe
updated 14.9 years ago by ▴ 930 • written 14.9 years ago by ▴ 230
0
votes
1
reply
1.1k
views
TranscriptDb and genomicranges questions
Cancer TranscriptDb Category IRanges GenomicRanges Cancer TranscriptDb Category IRanges
15.1 years ago Hervé Pagès 16k
0
votes
7
replies
1.8k
views
no summary of GOHyperGResult
GO GOstats Category GO GOstats Category
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 280
0
votes
0
replies
973
views
Problem about using "goProfiles"
Category goProfiles Category goProfiles
15.3 years ago wei tie ▴ 30
0
votes
3
replies
1.7k
views
genefilter findLargest and Illumina ids
Annotation Category Annotation Category
updated 15.4 years ago by ★ 1.2k • written 15.4 years ago by ▴ 480
0
votes
1
reply
872
views
KEGG overrepresentation loses genes
Annotation Category Annotation Category
updated 15.4 years ago by ★ 7.2k • written 15.4 years ago by ▴ 10
0
votes
1
reply
1.3k
views
filtering in GSEABase package
GO hgu95av2 mouse4302 PROcess Category GO hgu95av2 mouse4302 PROcess Category
updated 15.5 years ago by ▴ 610 • written 15.5 years ago by ▴ 190
0
votes
9
replies
2.9k
views
GSEA, topGO, GOstats...? what's a good way to look at GO over-representation?
affy Category nudge affy Category nudge
updated 15.6 years ago by ★ 13k • written 15.6 years ago by ★ 1.9k
0
votes
0
replies
661
views
GOstats testing using EntrezGene IDs not in chip-specific annotation package?
Annotation probe GOstats Category Annotation probe GOstats Category
15.6 years ago Marc Carlson ★ 7.2k
0
votes
3
replies
1.6k
views
GOHyperGResult in a data.frame, possible NAMESPACE problem?
GO Biobase annotate PROcess GOstats Category AnnotationDbi GO Biobase annotate PROcess
updated 15.7 years ago by ★ 7.4k • written 15.7 years ago by ★ 3.4k
0
votes
0
replies
978
views
Bioconductor Digest, Vol 83, Issue 4
GO biomaRt Category GO biomaRt Category
15.7 years ago Lavinia Gordon ▴ 480
0
votes
0
replies
1.2k
views
Fwd: [R] Question to use R plot GO pie chart
GO Cancer Category GO Cancer Category
15.7 years ago Waverley @ Palo Alto ▴ 10
0
votes
0
replies
1.2k
views
how to get gene list after hyperGTest (Yue, Chen - BMD)
Annotation Pathways affy GOstats Category AnnotationDbi Annotation Pathways affy GOstats
15.8 years ago Bucher Elmar ▴ 80
0
votes
2
replies
2.0k
views
Bioconductor Digest, Vol 82, Issue 20
Annotation Pathways affy GOstats Category AnnotationDbi Annotation Pathways affy GOstats
updated 15.8 years ago by ▴ 70 • written 15.8 years ago by ▴ 60
0
votes
1
reply
914
views
how to get gene list after hyperGTest
GOstats Category GOstats Category
updated 15.8 years ago by 68k • written 15.8 years ago by ▴ 60
0
votes
3
replies
1.6k
views
Hypergeometric Testing questions
GO GOstats Category GO GOstats Category
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ▴ 840
0
votes
1
reply
1.7k
views
FW: function error for "hyperGTest" in Category package
Annotation GO hgu133a probe GOstats Category Annotation GO hgu133a probe GOstats
updated 15.9 years ago by 25k • written 15.9 years ago by ▴ 60
0
votes
2
replies
1.8k
views
function error for "hyperGTest" in Category package
Annotation probe Category Annotation probe Category
updated 15.9 years ago by 6.7k • written 15.9 years ago by ▴ 60
0
votes
2
replies
1.1k
views
mislinked task views?
Cancer Category Cancer Category
updated 16.3 years ago by 6.7k • written 16.4 years ago by ▴ 180
0
votes
2
replies
1.2k
views
GO.db redundance
Annotation GO probe Category Annotation GO probe Category
updated 16.4 years ago by ★ 7.2k • written 16.4 years ago by ▴ 40
0
votes
1
reply
1.3k
views
GoStats - getting genes from categories
GO GOstats Category GO GOstats Category
updated 16.4 years ago by 68k • written 16.4 years ago by ▴ 330
0
votes
2
replies
1.1k
views
ChrMapHyperGParams and linearMTest in Category
Annotation GOstats Category Annotation GOstats Category
16.5 years ago Daren Tan ▴ 120
0
votes
0
replies
1.2k
views
hyperGTest, different Results using different annotation packages
Microarray Annotation GO ChipName db0 GOstats Category Microarray Annotation GO ChipName
16.5 years ago Wiebke Iffert ▴ 20
1
vote
0
replies
1.1k
views
RmiR, request for new package
miRNA Annotation GO cdf probe PROcess Category miRNA Annotation GO cdf probe PROcess
16.6 years ago Nishant Gopalakrishnan ▴ 340
0
votes
0
replies
1.1k
views
Gostats and custom list
Annotation Pathways GO Yeast convert GOstats Category Annotation Pathways GO Yeast
16.6 years ago Iain Wallace ▴ 50
0
votes
3
replies
1.5k
views
"Size" in summary() of "hyperGTest()
GO Category GO Category
updated 16.6 years ago by ★ 5.5k • written 16.6 years ago by ▴ 30
0
votes
0
replies
1.0k
views
hyperGTest on KEGG and PFAM with org.XX.eg annotations
Microarray Annotation Escherichia coli hgu95av2 Category Microarray Annotation hgu95av2
16.8 years ago Marc Carlson ★ 7.2k
0
votes
2
replies
1.6k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 16.9 years ago by ▴ 90 • written 16.9 years ago by ▴ 830
0
votes
0
replies
1.0k
views
adding KEGG annotations with ABPkBuilder from E.coli
Annotation annotate AnnBuilder PROcess Category Annotation annotate AnnBuilder PROcess
16.9 years ago Marc Carlson ★ 7.2k
0
votes
9
replies
1.8k
views
Help with 'annotation' in GOHyeprGParamsClass
Annotation GO Yeast Category Annotation GO Yeast Category
updated 16.9 years ago by ★ 5.5k • written 16.9 years ago by ▴ 50
0
votes
1
reply
999
views
Combining old Affy arrays for limma
rat2302 rgu34a rgu34b rgu34c affy limma Category rat2302 rgu34a rgu34b rgu34c affy
updated 16.9 years ago by 21k • written 16.9 years ago by ▴ 300
0
votes
1
reply
2.0k
views
problem with AnnotationDbi
ChipName db0 affy Category AnnotationDbi ChipName db0 affy Category AnnotationDbi
updated 16.9 years ago by 16k • written 16.9 years ago by ▴ 830
0
votes
5
replies
2.0k
views
problem with Category package and custom annotationDbi
Annotation Category AnnotationDbi Annotation Category AnnotationDbi
updated 16.9 years ago by ★ 5.5k • written 16.9 years ago by ▴ 830
0
votes
3
replies
1.7k
views
help with using Category package with makecdfenv built Gene ST package
GO cdf affy limma Category GO cdf affy limma Category
updated 16.9 years ago by ★ 5.5k • written 16.9 years ago by ▴ 830
0
votes
0
replies
1.0k
views
gseattperm return all NA
mouse4302 Category mouse4302 Category
16.9 years ago Saroj Mohapatra ▴ 450
159 results • Page 2 of 4
Recent ...
Replies
Comment: Visualization of Functional Enrichment Result with enrichplot: How to control la by zhaoqiansun0592 • 0
Wow, this is super helpful! I always struggle with label sizes in enrichplot. Glad to see a solution using gginnards([Pasjans][1]) and ggre…
Comment: Could we detect difference at pathway level but not significant different at gen by zhaoqiansun0592 • 0
Interesting question! It's cool that ChatGPT4 gave such a helpful answer. I've also been wondering if pathways([space waves][1]) can show d…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by zhaoqiansun0592 • 0
Good to know there are workarounds for these tricky [doodle baseball][1]! Thanks for sharing the tips! [1]: https://doodle-baseball.cc/
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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