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649
views
time course differential analysis - design matrix
GO GO
updated 11.6 years ago by 68k • written 11.6 years ago by ★ 13k
0
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0
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1.8k
views
[phenoTest package]: gsea.kegg error with absVals parameter
Pathways GO hgu133a hgu95av2 phenoTest Pathways GO hgu133a hgu95av2 phenoTest
11.6 years ago Kostas Kerkentzes ▴ 10
0
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0
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1.3k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
11.6 years ago James W. MacDonald 68k
0
votes
2
replies
2.7k
views
make.cdf.package Error in copySubstitute
GO cdf Biobase affy GO cdf Biobase affy
updated 11.6 years ago by 68k • written 11.6 years ago by ▴ 30
0
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1
reply
2.0k
views
GOseq at a specific level ?
GO goseq GO goseq
updated 11.6 years ago by ▴ 320 • written 11.7 years ago by ▴ 80
0
votes
3
replies
2.1k
views
Question about working with GRanges objects
GO GO
updated 11.6 years ago by ★ 11k • written 11.6 years ago by ▴ 180
0
votes
3
replies
3.1k
views
GOStats: summary hyperGTest, count and size
Annotation GO Organism GOstats Annotation GO Organism GOstats
11.6 years ago Christine Gläßer ▴ 60
0
votes
0
replies
2.1k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.6 years ago Magda Price ▴ 60
2
votes
8
replies
2.6k
views
Genes annotated to GO:0031281 using org.Hs.eg.db
GO Homo sapiens GO Homo sapiens
updated 11.6 years ago by 68k • written 11.6 years ago by ★ 1.1k
0
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5
replies
2.6k
views
TopGo package
GO topGO GO topGO
updated 11.6 years ago by ★ 8.2k • written 11.7 years ago by ▴ 20
0
votes
8
replies
5.6k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ★ 13k
0
votes
2
replies
3.1k
views
Questions about multi-factor contrast setting in DESeq2
GO Visualization Clustering limma edgeR DESeq2 GO Visualization Clustering limma edgeR
updated 11.7 years ago by ▴ 380 • written 11.7 years ago by 43k
0
votes
0
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2.6k
views
GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
11.7 years ago Dale Richardson ▴ 30
0
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4
replies
1.7k
views
svg error in arrayQualityMetrics
GO arrayQualityMetrics GO arrayQualityMetrics
updated 11.7 years ago by ▴ 750 • written 11.7 years ago by ▴ 300
0
votes
7
replies
2.6k
views
Low number of replicates DESeq
Transcription GO DESeq2 Transcription GO DESeq2
updated 11.7 years ago by 43k • written 11.7 years ago by ▴ 130
0
votes
3
replies
2.6k
views
pathview - plotting multiple samples in the same graph?
Pathways GO pathview Pathways GO pathview
11.7 years ago Peter Davidsen ▴ 210
0
votes
0
replies
1.2k
views
Significance of overlapping GO terms?
GO GO
11.7 years ago Tim Smith ★ 1.1k
0
votes
0
replies
2.4k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.7 years ago W. Evan Johnson ▴ 870
0
votes
1
reply
1.8k
views
Non-specific filtering of Affymetrix Microarray data
GO hgu95av2 GO hgu95av2
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ★ 13k
0
votes
1
reply
1.5k
views
fRMA- more issues with custom CDFs
GO probe frma GO probe frma
updated 11.7 years ago by ▴ 830 • written 11.7 years ago by ▴ 110
0
votes
0
replies
2.1k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.7 years ago Magda Price ▴ 60
0
votes
0
replies
1.7k
views
goseq: pwf: Error in if (hi <= low) { : missing value where TRUE/FALSE needed
RNASeq GO goseq DESeq2 RNASeq GO goseq DESeq2
11.7 years ago 刘鹏飞 ▴ 80
0
votes
0
replies
1.1k
views
DiffBind error loading dba
GO DiffBind NarrowPeaks GO DiffBind NarrowPeaks
11.7 years ago Rory Stark ★ 5.2k
0
votes
2
replies
1.4k
views
Can we use Intraclass correlation (ICC) to optimize clustering parameters?
GO Clustering rat2302 affy GO Clustering rat2302 affy
updated 11.7 years ago by ★ 4.2k • written 11.7 years ago by ★ 13k
0
votes
4
replies
1.6k
views
AgiMicroRna -1 filtered values
miRNA GO miRNA GO
11.8 years ago • updated 11.7 years ago Coonen Maarten TGX ▴ 30
0
votes
0
replies
882
views
error in DEXSeq fitDispersionFunction()
GO DEXSeq GO DEXSeq
11.7 years ago Wolfgang Huber ★ 13k
0
votes
7
replies
2.5k
views
Gene Ontology Annotations from Gene Names
Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats
updated 11.8 years ago by 68k • written 11.8 years ago by ★ 13k
0
votes
3
replies
2.2k
views
ReportingTools and gene annotation
Annotation GO cycle ReportingTools DESeq2 Annotation GO cycle ReportingTools DESeq2
updated 11.8 years ago by 68k • written 11.8 years ago by ▴ 340
0
votes
3
replies
2.4k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
updated 11.8 years ago by ▴ 20 • written 11.8 years ago by ★ 4.2k
0
votes
0
replies
873
views
How to compare GO results in goprofile
GO GO
11.8 years ago Bai, Bing ▴ 10
0
votes
0
replies
1.2k
views
Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
11.8 years ago Marc Carlson ★ 7.2k
0
votes
0
replies
2.4k
views
Pathview with minor species
Microarray Annotation GO Bacillus subtilis gage pathview Microarray Annotation GO gage
11.8 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.4k
views
Problem when trying to use \'affy\' package
Normalization GO affy sva SCAN.UPC Normalization GO affy sva SCAN.UPC
11.8 years ago Kaj Chokeshaiusaha ▴ 140
0
votes
5
replies
3.5k
views
DESeq2 - working with partial replicates
GO edgeR DESeq2 GO edgeR DESeq2
updated 11.8 years ago by 43k • written 11.8 years ago by ▴ 40
0
votes
0
replies
2.1k
views
edgeR - common dispersion and BCV
GO edgeR GO edgeR
11.8 years ago Avinash S ▴ 40
0
votes
3
replies
2.7k
views
Find enriched GO terms, given a list of GO terms of interest and background GO terms
Annotation GO topGO genomes Annotation GO topGO genomes
11.8 years ago Guest User ★ 13k
0
votes
4
replies
2.0k
views
Reading by column
GO GO
11.8 years ago Hajas, Wayne ▴ 30
0
votes
0
replies
2.7k
views
DESeq2 high fold change values for comparison of samples with zero counts
GO DESeq2 GO DESeq2
11.8 years ago Michael Love 43k
0
votes
3
replies
2.2k
views
Error in dispersionPlot using cummeRbund
GO cummeRbund GO cummeRbund
updated 11.8 years ago by ▴ 140 • written 11.8 years ago by ★ 13k
0
votes
2
replies
1.6k
views
Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Annotation GO BSgenome TranscriptDb BSgenome GenomicFeatures Annotation GO BSgenome
updated 11.9 years ago by 16k • written 11.9 years ago by ▴ 60
0
votes
1
reply
2.7k
views
gage and GO analysis
GO convert gage GO convert gage
updated 11.9 years ago by ▴ 570 • written 11.9 years ago by ★ 13k
0
votes
1
reply
1.9k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 11.9 years ago by 68k • written 11.9 years ago by ★ 13k
0
votes
1
reply
1.8k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 11.9 years ago by ▴ 1000 • written 11.9 years ago by ▴ 80
0
votes
1
reply
1.4k
views
topGO spurious GO terms?
Pathways GO topGO Pathways GO topGO
updated 11.9 years ago by ▴ 50 • written 11.9 years ago by ★ 13k
0
votes
1
reply
5.8k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 11.9 years ago by ▴ 280 • written 11.9 years ago by 16k
0
votes
0
replies
2.3k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
11.9 years ago Hervé Pagès 16k
0
votes
1
reply
1.6k
views
Questions on Combat in methylation data Thank you for your help
GO sva GO sva
updated 11.9 years ago by ▴ 440 • written 11.9 years ago by ▴ 870
0
votes
0
replies
2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.9 years ago Hervé Pagès 16k
0
votes
1
reply
1.0k
views
remove evidence Codes
GO GO
updated 11.9 years ago by 6.7k • written 11.9 years ago by ▴ 190
0
votes
1
reply
1.7k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 11.9 years ago by ▴ 320 • written 11.9 years ago by 53k
1,936 results • Page 6 of 39
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
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Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
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Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
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Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
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Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
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Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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