Showing : GO • reset
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Summarizing Single-channel Agilent data
GO limma GO limma
13.7 years ago Gordon Smyth 53k
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GAGE heatmap pdf question...
GO gage GO gage
13.7 years ago Alan Derr ▴ 50
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1.6k
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Summarizing Single-channel Agilent data
GO GO
updated 13.7 years ago by ★ 1.1k • written 13.7 years ago by ▴ 280
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2.1k
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problem creating own org.Ss.eg.db
Annotation GO Organism OrgDb Annotation GO Organism OrgDb
updated 13.7 years ago by ★ 4.1k • written 13.7 years ago by ★ 7.2k
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PostForm() with KEGG
GO Cancer KEGGSOAP GO Cancer KEGGSOAP
13.7 years ago Voke AO ▴ 760
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6.4k
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how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 3.4 years ago by • 0 • written 13.7 years ago by ★ 7.2k
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750
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adding factors to a data frame from a dataframe
GO Cancer GO Cancer
13.7 years ago Tom Keller ▴ 70
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1.2k
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adding factors to a data frame from a dataframe
GO GO
updated 13.7 years ago by 25k • written 13.7 years ago by ▴ 70
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1.0k
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about GO analysis
GO Visualization GO Visualization
13.7 years ago Zhi Zhang ▴ 70
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3
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1.4k
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how to get gene list for given GO terms?
GO GO
updated 13.7 years ago by 25k • written 13.7 years ago by ★ 1.3k
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1.5k
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problem creating own org.Ss.eg.db
Annotation GO Annotation GO
13.7 years ago Guido Hooiveld ★ 4.1k
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6
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1.8k
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Making use of the Apis mellifera assembly 2 data in goSeq
GO Organism Apis mellifera goseq GO Organism Apis mellifera goseq
updated 13.7 years ago by 16k • written 13.7 years ago by ▴ 30
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings BSgenome rtracklayer goseq GO
13.7 years ago Alicia Oshlack ▴ 100
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1.0k
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO
13.8 years ago Hervé Pagès 16k
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1.7k
views
GO Analysis for Mouse Exon Array
Annotation Pathways GO limma GOstats oligo Annotation Pathways GO limma GOstats oligo
updated 13.8 years ago by ★ 4.3k • written 13.8 years ago by ▴ 60
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2.0k
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Deferential gene expression databases
Microarray Genetics Annotation Normalization Pathways GO Cancer BSgenome probe annotate
13.8 years ago saikouy bah ▴ 30
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2
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1.9k
views
ChIPpeakAnno
GO BSgenome annotate BSgenome ChIPpeakAnno GO BSgenome annotate BSgenome ChIPpeakAnno
updated 13.8 years ago by ▴ 10 • written 13.8 years ago by ▴ 10
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13
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3.2k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 30
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2
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7.1k
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gplots Heatmap
SNP Transcription Sequencing RNASeq miRNA Microarray Annotation Normalization GO Cancer
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 10
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2
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Creating a customized cut flow with the affy/limma packages
GO limma ASSIGN GO limma ASSIGN
updated 13.8 years ago by 68k • written 13.8 years ago by ▴ 20
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1.3k
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Creating a customized cut flow with the affy/limma packages
GO hgu133plus2 limma ASSIGN GO hgu133plus2 limma ASSIGN
updated 13.8 years ago by 68k • written 13.8 years ago by ★ 13k
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2
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1.1k
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Two populations on microarray
Microarray Normalization GO probe limma Microarray Normalization GO probe limma
updated 13.8 years ago by ★ 6.0k • written 13.8 years ago by ▴ 60
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1
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1.3k
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GOseq error
GO goseq GO goseq
updated 13.8 years ago by ▴ 930 • written 13.8 years ago by ▴ 100
0
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7
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1.7k
views
gene function assessment
Annotation GO Annotation GO
updated 13.8 years ago by 21k • written 13.8 years ago by ▴ 410
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0
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886
views
GOSeq error
GO goseq GO goseq
13.8 years ago Iain Gallagher ▴ 930
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1
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1.6k
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NormqPCR and ReadqPCR
GO ReadqPCR NormqPCR GO ReadqPCR NormqPCR
updated 13.8 years ago by ▴ 300 • written 13.8 years ago by ▴ 10
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3.1k
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Proxy setting for R/Bioconductor
GO GO
updated 13.8 years ago by 6.7k • written 13.8 years ago by ▴ 10
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2
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989
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Cross-comparison of independent intensities from different experiments (genepix) (sorry I don\'t know how to describe the problem better)
Normalization GO Normalization GO
updated 13.8 years ago by 68k • written 13.8 years ago by ★ 13k
1
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TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
13.8 years ago Paul Geeleher ★ 1.3k
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812
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create GeneSetCollection from OBOCollection
GO convert GOstats GO convert GOstats
13.8 years ago Marc Carlson ★ 7.2k
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1.5k
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
13.8 years ago Valerie Obenchain ★ 6.8k
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1.7k
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refseq to genesymbol with BiomaRt - problem occurs
GO hgu133plus2 PROcess convert biomaRt GO hgu133plus2 PROcess convert biomaRt
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 240
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0
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1.3k
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DESeq estimateDispersion query
GO edgeR DESeq GO edgeR DESeq
13.8 years ago Iain Gallagher ▴ 930
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2.3k
views
FW: URGENT Help required: Getting this error with GAGE analysis, input files attached
Microarray Annotation Pathways GO Cancer Breast cycle gage Microarray Annotation GO
updated 13.8 years ago by ▴ 200 • written 13.8 years ago by 25k
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3
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1.0k
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miRNA normalisation
GO probe GO probe
updated 13.8 years ago by 68k • written 13.8 years ago by ▴ 40
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889
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create GeneSetCollection from OBOCollection
GO convert GOstats GO convert GOstats
13.8 years ago Wendy Qiao ▴ 360
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1.8k
views
GAGE vs other GO analysis tools
Microarray Pathways GO gage Microarray Pathways GO gage
updated 13.8 years ago by ★ 1.6k • written 13.8 years ago by ▴ 240
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3
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How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
Microarray GO Cancer Breast gage Microarray GO Cancer Breast gage
updated 13.9 years ago by ▴ 200 • written 13.9 years ago by ★ 6.8k
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ChiPpeakAnno: findOverlappingPeaks: running time
GO ChIPpeakAnno GO ChIPpeakAnno
updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ★ 13k
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1.4k
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[R-sig-hpc] About Multicore: mclapply
GO Cancer GO Cancer
13.9 years ago Martin Morgan 25k
0
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1
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938
views
DESeq mean,var
RNASeq GO DESeq RNASeq GO DESeq
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 50
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1
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910
views
How remove controls probes - Affymetrix Gene
GO probe oligo GO probe oligo
updated 13.9 years ago by 68k • written 13.9 years ago by ★ 13k
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2
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1.3k
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RMA normalisation of test microarray data to training data
Microarray GO Cancer affy Microarray GO Cancer affy
updated 13.9 years ago by 68k • written 13.9 years ago by ★ 1.9k
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2
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1.3k
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question subsetting expressionSet
GO convert GO convert
updated 13.9 years ago by ▴ 550 • written 13.9 years ago by ★ 4.1k
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1
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3.3k
views
Heatmap.2 Trace Line Thickness
GO GO
updated 13.9 years ago by ▴ 350 • written 13.9 years ago by ▴ 10
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1
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2.1k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 13.9 years ago by ▴ 350 • written 13.9 years ago by ▴ 10
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3
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1.7k
views
Problems selecting rows from dataframe (exprs) of GNF Atlas data....
GO probe GEOquery GO probe GEOquery
updated 13.9 years ago by ▴ 60 • written 13.9 years ago by ▴ 150
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3
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1.5k
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Problems selecting rows from dataframe (exprs) of GNF Atlas data....
GO probe GEOquery GO probe GEOquery
updated 13.9 years ago by ▴ 60 • written 13.9 years ago by ▴ 150
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0
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1.3k
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Difference between go, with_go and with_go_go
GO biomaRt GO biomaRt
13.9 years ago Marc Carlson ★ 7.2k
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1.7k
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limma - 2-color agilent microarray, GO annotation
Microarray Annotation GO Organism limma GOstats oligo ASSIGN Microarray Annotation GO
13.9 years ago Gordon Smyth 53k
1,936 results • Page 14 of 39
Recent ...
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
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