Showing : category • reset
1
vote
1
reply
456
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 3.2 years ago by 44k • written 3.2 years ago by • 0
0
votes
3
replies
1.3k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 4.3 years ago by ▴ 340 • written 4.4 years ago by ▴ 10
0
votes
4
replies
4.1k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO Category goseq GO Category goseq
updated 5.6 years ago by ▴ 10 • written 10.1 years ago by ▴ 10
1
vote
0
replies
919
views
enrichment analysis for gene pairs
go gostats category gsea
6.0 years ago Hector Corrada Bravo ▴ 60
0
votes
0
replies
818
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
6.2 years ago petyuk ▴ 70
0
votes
8
replies
1.2k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 930
2
votes
2
replies
629
views
rownames for categoryReshape
Category
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
1
vote
0
replies
794
views
how to fetch GO categories from Chinese hamster genome
GO Category goseq
7.1 years ago upendra kumar devisetty ▴ 30
0
votes
1
reply
880
views
GO enrichment
GO Category goseq GO Category goseq
7.2 years ago Guest User ★ 12k
0
votes
1
reply
1.0k
views
snpStats reference allele used in genetic associations?
SNP Category snpStats SNP Category snpStats
updated 7.4 years ago by 6.5k • written 7.4 years ago by ★ 12k
0
votes
0
replies
1.3k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
7.6 years ago Magda Price ▴ 60
0
votes
8
replies
3.6k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 7.6 years ago by 13k • written 7.6 years ago by ★ 12k
0
votes
0
replies
1.4k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
7.7 years ago W. Evan Johnson ▴ 840
0
votes
0
replies
1.2k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
7.7 years ago Magda Price ▴ 60
0
votes
0
replies
1.2k
views
R pathview and mouse
Category pathview Category pathview
7.8 years ago Luo Weijun ★ 1.5k
0
votes
1
reply
1.3k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 7.9 years ago by ▴ 80 • written 7.9 years ago by ▴ 20
0
votes
4
replies
2.8k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation Normalization hgu133plus2 affy PROcess Category Annotation Normalization affy
updated 7.9 years ago by 58k • written 7.9 years ago by ★ 12k
0
votes
1
reply
701
views
GSEABase error parsing msigdb_v4.0.xml
Category Category
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 10
0
votes
0
replies
847
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
8.0 years ago Gordon Smyth 44k
0
votes
0
replies
727
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
8.0 years ago Pekka Kohonen ▴ 190
0
votes
1
reply
610
views
Which package I should use
Sequencing Category Sequencing Category
updated 8.1 years ago by ▴ 30 • written 8.1 years ago by ▴ 10
0
votes
7
replies
3.5k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 8.1 years ago by ▴ 460 • written 8.1 years ago by ▴ 580
0
votes
1
reply
1.0k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 8.2 years ago by ★ 6.7k • written 8.2 years ago by ▴ 20
0
votes
0
replies
833
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category BEAT Category BEAT
8.4 years ago Hin-Tak Leung ▴ 30
0
votes
0
replies
712
views
Diff Bind consultation
Category DiffBind Category DiffBind
8.5 years ago Rory Stark ★ 4.1k
0
votes
0
replies
687
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
8.5 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
733
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category Category
updated 8.6 years ago by ▴ 60 • written 8.6 years ago by ▴ 30
0
votes
6
replies
692
views
Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 8.7 years ago by 58k • written 8.7 years ago by ★ 12k
0
votes
2
replies
1.1k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 80
0
votes
2
replies
770
views
Difficulties in using the mgsa package for Gene Set Analysis
GO rat2302 Category mgsa GO rat2302 Category mgsa
updated 8.8 years ago by ▴ 60 • written 8.8 years ago by ★ 12k
0
votes
0
replies
516
views
ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
9.0 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
528
views
HyperGTest 'count' value
Annotation Category Annotation Category
9.0 years ago Mary Kindall ▴ 70
0
votes
0
replies
444
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
9.1 years ago Gordon Smyth 44k
0
votes
2
replies
579
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
updated 9.2 years ago by 44k • written 9.2 years ago by ▴ 80
0
votes
3
replies
1.4k
views
oligo and pd.aragene.1.1.st annotation
Annotation limma Category pdInfoBuilder Annotation limma Category pdInfoBuilder
updated 9.2 years ago by ★ 7.2k • written 9.2 years ago by ▴ 20
0
votes
2
replies
584
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 9.3 years ago by 13k • written 9.3 years ago by ▴ 190
0
votes
3
replies
758
views
GOstats - internal filtering?
Annotation GO hgu133plus2 GOstats Category Annotation GO hgu133plus2 GOstats Category
updated 9.5 years ago by 58k • written 9.5 years ago by ▴ 120
0
votes
0
replies
692
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
9.5 years ago Gita Singh ▴ 10
0
votes
3
replies
1.2k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe limma Category probe limma Category
updated 9.6 years ago by 58k • written 9.6 years ago by ▴ 10
0
votes
0
replies
800
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
9.6 years ago Matthew Young ▴ 50
1
vote
0
replies
1.4k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
9.7 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.1k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 9.8 years ago by ▴ 350 • written 9.8 years ago by ▴ 10
0
votes
1
reply
1.8k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ▴ 10
0
votes
2
replies
1.4k
views
retrieve the level for a GO category
GO Category GO Category
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 150
0
votes
9
replies
904
views
problem with GO terms
GO GOstats Category GO GOstats Category
updated 9.9 years ago by 58k • written 9.9 years ago by ▴ 610
0
votes
0
replies
691
views
goSeq error (steve Shen)
GO Category edgeR goseq GO Category edgeR goseq
10.0 years ago Alicia Oshlack ▴ 100
0
votes
4
replies
1.4k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 10.0 years ago by ▴ 30 • written 10.0 years ago by 44k
0
votes
0
replies
866
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category edgeR Category edgeR
10.0 years ago Emanuel Heitlinger ▴ 30
0
votes
2
replies
1.4k
views
RNA seq analysis of Arabidopsis genome
GO Category goseq GO Category goseq
updated 10.1 years ago by ▴ 50 • written 10.1 years ago by ▴ 10
0
votes
0
replies
817
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
10.1 years ago Lavorgna Giovanni ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2/edgeR/limma help with most appropriate design matrix by Gordon Smyth 44k
I have added a suggestion about an alternative representation without the intercept that might help you.
Answer: Problem select / ensembl package by yinnahm • 0
ensembldb::select works perfect Thanks!!!
Comment: How to add pseudocount to DESeq2 dds object by Stanley • 0
In most cases, yes- a sample that gives a 0 for a gene has high counts elsewhere. I actually performed a PCA early on for my sample-leve…
Answer: Difficulty dowloading hg38 cnv data in tcgabiolinks by Tiago C. Silva ▴ 150
I just added suport to this data type query.cnv <- GDCquery( project = "TCGA-ESCA", data.category = "Copy Numbe…
Comment: DESeq2/edgeR/limma help with most appropriate design matrix by rebecca.lea.johnston • 0
Thank you so much for your response Gordon, I truly appreciate it! Also glad to hear my design matrix is correct in this context :)
Votes
Comment: DESeq2/edgeR/limma help with most appropriate design matrix
Bioconductor 3.14 is Released!
Bioconductor 3.14 is Released!
Bioconductor 3.14 is Released!
Answer: DESeq2/edgeR/limma help with most appropriate design matrix
Awards • All
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