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convert
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reset
3
votes
1
reply
13k
views
convert data in to expression set
limma
convert
limma
convert
updated 10.8 years ago by
Jeremy Ng
▴ 180 • written 10.8 years ago by
Nikul Soni
▴ 80
0
votes
0
replies
12k
views
Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
Cancer
convert
Cancer
convert
12.4 years ago
Chao-Jen Wong
▴ 580
1
vote
2
replies
12k
views
Mapping gene symbols to gene names (org.Hs.eg.db?)
convert
convert
updated 9.9 years ago by
James W. MacDonald
65k • written 9.9 years ago by
Tim Smith
★ 1.1k
0
votes
3
replies
12k
views
Convert gene symbols to ensembl id
convert
convert
updated 11.9 years ago by
Fred Boehm
▴ 20 • written 11.9 years ago by
michelle_low
▴ 50
0
votes
3
replies
11k
views
How to combine expression values of multiple probes for one gene
probe
convert
geneexpression
onechannelgui
updated 8.7 years ago by
svlachavas
▴ 830 • written 8.7 years ago by
ayanava18
▴ 10
0
votes
3
replies
7.0k
views
converting GEO soft files to MS excel files
convert
convert
updated 17.3 years ago by
Sean Davis
21k • written 17.3 years ago by
Dr Gyorffy Balazs
▴ 320
0
votes
3
replies
6.7k
views
org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Cancer
Homo sapiens
convert
Cancer
Homo sapiens
convert
updated 15.1 years ago by
Seraya Maouche
▴ 10 • written 15.1 years ago by
Tim Smith
★ 1.1k
0
votes
21
replies
6.4k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 4 months ago by
Marge
• 0 • written 11.2 years ago by
José Luis Lavín
▴ 280
1
vote
2
replies
6.0k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 15 months ago by
snijesh
▴ 20 • written 6.3 years ago by
p_donchev84
• 0
0
votes
5
replies
6.0k
views
How to reverse translate amino acid sequence into mammalian codon optimised cDNA
convert
translation
written 9.4 years ago by
tomas.bjorklund
▴ 20
0
votes
4
replies
5.3k
views
GRanges - coercion from dataframe
convert
IRanges
convert
IRanges
12.3 years ago
Fahim Md
▴ 250
0
votes
0
replies
5.0k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
14.6 years ago
Michael Dondrup
▴ 140
0
votes
1
reply
4.6k
views
Converting Genotyping result for PLINK
convert
convert
updated 14.4 years ago by
Claus-Jürgen Scholz
▴ 90 • written 14.4 years ago by
Peter Ganske
▴ 50
0
votes
4
replies
4.3k
views
GEOquery
convert
GEOquery
convert
GEOquery
updated 14.0 years ago by
Sean Davis
21k • written 14.0 years ago by
Julie Zhu
★ 4.3k
0
votes
2
replies
4.3k
views
Duplicated Gene IDs - averaging
convert
metaArray
convert
metaArray
12.5 years ago
boczniak767
▴ 720
0
votes
11
replies
4.0k
views
creating GRanges and reading BAM files
Coverage
convert
Coverage
convert
updated 12.1 years ago by
Sunny Yu Liu
▴ 80 • written 12.1 years ago by
David A.
▴ 70
0
votes
1
reply
3.7k
views
samtools error
Cancer
convert
Cancer
convert
updated 11.8 years ago by
Lucia Peixoto
▴ 330 • written 11.8 years ago by
Marcus Davy
▴ 390
0
votes
5
replies
3.6k
views
how to convert genotype snp matrix to nucleotide genotypes?
SNP
convert
snpMatrix
SNP
convert
snpMatrix
updated 10.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.9 years ago by
Tereza Jezkova UNLV
▴ 20
0
votes
8
replies
3.6k
views
DESeq and transcript-wise analysis
convert
DESeq
convert
DESeq
12.1 years ago
Elena Sorokin
▴ 150
0
votes
1
reply
3.5k
views
writing BAM files from within R
convert
Rsamtools
convert
Rsamtools
updated 12.2 years ago by
Valerie Obenchain
★ 6.8k • written 12.2 years ago by
margherita mutarelli
▴ 10
0
votes
3
replies
3.5k
views
How to deal with Affymetrix probe that map to multiple genes
GO
Clustering
probe
convert
GO
Clustering
probe
convert
10.6 years ago
Gundala Viswanath
▴ 230
0
votes
1
reply
3.5k
views
problems generating a gene2GOlist in topGO
Genetics
Annotation
GO
hgu95av2
convert
biomaRt
topGO
Genetics
Annotation
GO
hgu95av2
updated 12.0 years ago by
Adrian Alexa
▴ 400 • written 12.0 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
5
replies
3.4k
views
Adjacency to network using R
Visualization
Network
convert
Visualization
Network
convert
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
pankaj borah
▴ 120
0
votes
3
replies
3.4k
views
convert affy CEL files to data.frame??
convert
convert
updated 5.6 years ago by
giulio.genovese
• 0 • written 13.2 years ago by
D M
▴ 40
0
votes
4
replies
3.3k
views
How to combine VCF-class and data.frame with annotations
GO
annotate
convert
ggbio
GO
annotate
convert
ggbio
written 11.6 years ago by
Stefan Dentro
▴ 70
1
vote
2
replies
3.3k
views
minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO
convert
minfi
bumphunter
GO
convert
minfi
bumphunter
updated 8.2 years ago by
david.watson
▴ 30 • written 9.9 years ago by
Guido Hooiveld
★ 3.9k
3
votes
1
reply
3.2k
views
convert GeneSetCollection to a list
convert
convert
updated 12.4 years ago by
Robert Castelo
★ 3.1k • written 12.4 years ago by
Wendy Qiao
▴ 360
0
votes
6
replies
3.2k
views
LogFC query in Limma
Pathways
convert
Pathways
convert
updated 11.2 years ago by
Steve Lianoglou
★ 13k • written 11.2 years ago by
Roopa Subbaiaih
▴ 130
0
votes
6
replies
3.2k
views
converting probeset id to gene id's : fRMA
probe
affy
convert
frma
probe
affy
convert
frma
updated 9.8 years ago by
Peter Langfelder
★ 2.9k • written 9.8 years ago by
Abhishek Pratap
▴ 190
0
votes
8
replies
3.1k
views
Reading Agilent files using read.maimages
Survival
DynDoc
genefilter
tkWidgets
affy
vsn
marray
convert
ArrayExpress
Survival
affy
updated 16.6 years ago by
Scott Reagan Franklin
▴ 20 • written 16.6 years ago by
Steve Taylor
▴ 100
0
votes
1
reply
3.1k
views
RE : create an new AnnotatedDataFrame
Annotation
Survival
Yeast
Biobase
genefilter
tkWidgets
marray
convert
arrayMagic
affyio
updated 16.6 years ago by
Martin Morgan
25k • written 16.6 years ago by
Yad Ghavi-Helm
▴ 30
0
votes
21
replies
3.1k
views
How to annotate genomic coordinates
convert
convert
11.4 years ago
José Luis Lavín
▴ 280
1
vote
2
replies
3.0k
views
GenBank RefSeq conversion
convert
convert
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
Eleni Christodoulou
▴ 150
0
votes
2
replies
3.0k
views
error with as.numeric when running pvclust
convert
convert
updated 11.4 years ago by
James W. MacDonald
65k • written 11.4 years ago by
Alyaa Mahmoud
▴ 440
6
votes
1
reply
3.0k
views
[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing
Annotation
convert
biomaRt
ReportingTools
DESeq2
Sequencing
Annotation
convert
updated 9.2 years ago by
andrew.j.skelton73
▴ 370 • written 10.3 years ago by
Jason Hackney
▴ 160
0
votes
4
replies
3.0k
views
450k annotation packages compatible version and analysis with blockFinder (minfi)
Annotation
Clustering
convert
minfi
Annotation
Clustering
convert
minfi
updated 10.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.4 years ago by
Florence Cavalli
▴ 50
0
votes
5
replies
3.0k
views
fastq files
convert
convert
updated 13.1 years ago by
Martin Morgan
25k • written 13.1 years ago by
David
▴ 860
0
votes
2
replies
2.9k
views
converting transcripts to gene level
convert
convert
updated 12.2 years ago by
Michael Lawrence
★ 11k • written 12.2 years ago by
Abhishek Pratap
▴ 410
0
votes
6
replies
2.9k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
updated 10.1 years ago by
James W. MacDonald
65k • written 10.1 years ago by
Guest User
★ 13k
0
votes
5
replies
2.9k
views
vsn: meanSdPlot + MAlist
Normalization
vsn
limma
convert
Normalization
vsn
limma
convert
updated 14.4 years ago by
Martin Morgan
25k • written 14.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
2
replies
2.9k
views
Biomart annotation
annotate
convert
annotate
convert
updated 9.7 years ago by
John Blischak
▴ 190 • written 9.7 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
2.7k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 15 months ago by
Gordon Smyth
50k • written 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
3
replies
2.7k
views
how to convert ExpressionSet to AffyBatch
convert
convert
updated 10.6 years ago by
James W. MacDonald
65k • written 10.6 years ago by
wang peter
★ 2.0k
0
votes
1
reply
2.7k
views
limma topTable annotation
GO
hgu133plus2
affy
limma
convert
Category
GO
hgu133plus2
affy
limma
convert
Category
updated 13.1 years ago by
David Iles
▴ 130 • written 13.1 years ago by
Gordon Smyth
50k
1
vote
1
reply
2.6k
views
MethyLumiSet object
convert
genoset
minfi
convert
genoset
minfi
11.0 years ago
Tim Triche
★ 4.2k
0
votes
12
replies
2.6k
views
BioMart and Ensembl questions
convert
biomaRt
convert
biomaRt
updated 14.5 years ago by
Paul Leo
▴ 970 • written 14.6 years ago by
jiayu wen
▴ 10
0
votes
3
replies
2.6k
views
[GSVA] Segfault with GSVA
RNASeq
Microarray
Annotation
gcrma
convert
GSVA
RNASeq
Microarray
Annotation
gcrma
GSVA
updated 11.2 years ago by
capricy gao
▴ 230 • written 11.2 years ago by
Robert Castelo
★ 3.1k
0
votes
3
replies
2.6k
views
Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol
convert
convert
10.6 years ago
Gundala Viswanath
▴ 230
0
votes
5
replies
2.6k
views
summarizeOverlaps using GRanges or bed file as reads?
convert
convert
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
1
reply
2.5k
views
samtools error
convert
convert
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
Yu Chuan Tai
▴ 440
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
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mercedeh.movassagh
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Yes that is correct
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It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
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This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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