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1
vote
1
reply
1.2k
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
0
votes
3
replies
2.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 6.8 years ago by ▴ 360 • written 6.9 years ago by ▴ 10
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 12.6 years ago by ▴ 10
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go gostats category gsea
8.5 years ago Hector Corrada Bravo ▴ 60
0
votes
0
replies
1.3k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
8.7 years ago petyuk ▴ 70
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
2
votes
2
replies
1.1k
views
rownames for categoryReshape
Category
updated 9.4 years ago by 25k • written 9.4 years ago by • 0
1
vote
0
replies
1.2k
views
how to fetch GO categories from Chinese hamster genome
GO Category goseq
9.6 years ago upendra kumar devisetty ▴ 30
0
votes
1
reply
1.4k
views
GO enrichment
GO Category goseq GO Category goseq
9.7 years ago Guest User ★ 13k
0
votes
1
reply
1.6k
views
snpStats reference allele used in genetic associations?
SNP Category snpStats SNP Category snpStats
updated 9.9 years ago by 6.7k • written 9.9 years ago by ★ 13k
0
votes
0
replies
1.8k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.1 years ago Magda Price ▴ 60
0
votes
8
replies
4.8k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
0
votes
0
replies
2.0k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.2 years ago W. Evan Johnson ▴ 850
0
votes
0
replies
1.7k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.2 years ago Magda Price ▴ 60
0
votes
0
replies
1.7k
views
R pathview and mouse
Category pathview Category pathview
10.3 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
2.0k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 10.4 years ago by ▴ 80 • written 10.4 years ago by ▴ 20
0
votes
4
replies
3.6k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation Normalization hgu133plus2 affy PROcess Category Annotation Normalization affy
updated 10.4 years ago by 65k • written 10.4 years ago by ★ 13k
0
votes
1
reply
1.0k
views
GSEABase error parsing msigdb_v4.0.xml
Category Category
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
1.2k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
10.5 years ago Pekka Kohonen ▴ 190
0
votes
1
reply
929
views
Which package I should use
Sequencing Category Sequencing Category
updated 10.6 years ago by ▴ 30 • written 10.6 years ago by ▴ 10
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 10.6 years ago by ▴ 470 • written 10.6 years ago by ▴ 660
0
votes
1
reply
1.4k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by ▴ 20
0
votes
0
replies
1.3k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category BEAT Category BEAT
10.9 years ago Hin-Tak Leung ▴ 30
0
votes
0
replies
1.1k
views
Diff Bind consultation
Category DiffBind Category DiffBind
11.0 years ago Rory Stark ★ 5.2k
0
votes
0
replies
1.0k
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
11.0 years ago Julie Zhu ★ 4.3k
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
6
replies
1.1k
views
Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 11.2 years ago by 65k • written 11.2 years ago by ★ 13k
0
votes
2
replies
1.6k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO rat2302 Category mgsa GO rat2302 Category mgsa
updated 11.3 years ago by ▴ 60 • written 11.3 years ago by ★ 13k
0
votes
0
replies
811
views
ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
11.5 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
902
views
HyperGTest 'count' value
Annotation Category Annotation Category
11.5 years ago Mary Kindall ▴ 70
0
votes
0
replies
701
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
11.6 years ago Gordon Smyth 50k
0
votes
2
replies
967
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
updated 11.7 years ago by 50k • written 11.7 years ago by ▴ 80
0
votes
3
replies
2.0k
views
oligo and pd.aragene.1.1.st annotation
Annotation limma Category pdInfoBuilder Annotation limma Category pdInfoBuilder
updated 11.7 years ago by ★ 7.2k • written 11.7 years ago by ▴ 20
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
3
replies
1.3k
views
GOstats - internal filtering?
Annotation GO hgu133plus2 GOstats Category Annotation GO hgu133plus2 GOstats Category
updated 12.0 years ago by 65k • written 12.0 years ago by ▴ 120
0
votes
0
replies
1.1k
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
12.0 years ago Gita Singh ▴ 10
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
0
replies
1.2k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
12.1 years ago Matthew Young ▴ 50
1
vote
0
replies
2.1k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
12.2 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.6k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 12.3 years ago by ▴ 350 • written 12.3 years ago by ▴ 10
0
votes
1
reply
2.3k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 10
0
votes
2
replies
1.8k
views
retrieve the level for a GO category
GO Category GO Category
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 150
0
votes
9
replies
1.6k
views
problem with GO terms
GO GOstats Category GO GOstats Category
updated 12.4 years ago by 65k • written 12.4 years ago by ▴ 620
0
votes
0
replies
1.1k
views
goSeq error (steve Shen)
GO Category edgeR goseq GO Category edgeR goseq
12.5 years ago Alicia Oshlack ▴ 100
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
0
replies
1.1k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category edgeR Category edgeR
12.5 years ago Emanuel Heitlinger ▴ 30
0
votes
2
replies
2.2k
views
RNA seq analysis of Arabidopsis genome
GO Category goseq GO Category goseq
updated 12.6 years ago by ▴ 50 • written 12.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
12.6 years ago Lavorgna Giovanni ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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