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1.6k
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get synthetic exon dataset with easyRNASeq
RNASeq
Alignment
Annotation
Normalization
GO
PROcess
GenomicRanges
DEXSeq
easyRNASeq
GO
13.2 years ago
delhomme@embl.de
★ 1.2k
0
votes
0
replies
1.9k
views
Classification in Mass Spectrometry Data
Microarray
Classification
Cancer
Ovarian
PROcess
MLInterfaces
ASSIGN
Microarray
Cancer
13.2 years ago
McGee, Monnie
▴ 300
0
votes
1
reply
999
views
a question about the low level match function
PROcess
PROcess
updated 13.2 years ago by
Harris A. Jaffee
▴ 590 • written 13.2 years ago by
wang peter
★ 2.0k
0
votes
0
replies
1.4k
views
Removing overlapping genes from annotation for RNAseq read count
RNASeq
Annotation
PROcess
DESeq
RNASeq
Annotation
PROcess
DESeq
13.2 years ago
Guest User
★ 13k
0
votes
4
replies
2.5k
views
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
13.2 years ago
Ricardo Silva
▴ 110
0
votes
5
replies
2.0k
views
frma for Nimblegen arrays?
Microarray
Normalization
affy
PROcess
safe
frma
Microarray
Normalization
affy
PROcess
updated 13.3 years ago by
Matthew McCall
▴ 830 • written 13.3 years ago by
wrighth
▴ 260
0
votes
1
reply
925
views
annotation package building
Annotation
Organism
PROcess
Annotation
Organism
PROcess
updated 13.3 years ago by
Marc Carlson
★ 7.2k • written 13.3 years ago by
Ingrid Mercier
▴ 60
0
votes
0
replies
1.9k
views
450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Annotation
db0
probe
annotate
PROcess
GenomicFeatures
GenomicRanges
Annotation
db0
probe
13.3 years ago
Marc Carlson
★ 7.2k
0
votes
0
replies
1.2k
views
get synthetic exon dataset with easyRNASeq
RNASeq
Annotation
Normalization
GO
PROcess
easyRNASeq
RNASeq
Annotation
Normalization
GO
13.3 years ago
delhomme@embl.de
★ 1.2k
0
votes
3
replies
1.3k
views
DEXSeq offset term
Normalization
PROcess
DEXSeq
Normalization
PROcess
DEXSeq
updated 13.3 years ago by
Alejandro Reyes
★ 1.9k • written 13.3 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
warnings on easyRNASeq package
Annotation
Organism
PROcess
GenomicRanges
easyRNASeq
Annotation
Organism
PROcess
updated 13.3 years ago by
Mun Hua Tan
▴ 10 • written 13.3 years ago by
delhomme@embl.de
★ 1.2k
0
votes
1
reply
1.6k
views
(microarray) - affylmGUI error when reading Affymetrix U133A and U133B .CEL file
Microarray
PROcess
affylmGUI
Microarray
PROcess
affylmGUI
updated 13.4 years ago by
James W. MacDonald
68k • written 13.4 years ago by
Zack Will
▴ 30
0
votes
0
replies
1.4k
views
Fwd: ASSIST on contrast matrix
Network
Homo sapiens
limma
PROcess
Network
Homo sapiens
limma
PROcess
13.4 years ago
Seyed Ahmad Mousavi
▴ 10
0
votes
1
reply
926
views
readPositonalinfo
PROcess
PROcess
updated 13.4 years ago by
Dario Strbenac
★ 1.6k • written 13.4 years ago by
adesh ashok
▴ 30
0
votes
1
reply
1.2k
views
readPositionalInfo
PROcess
PROcess
updated 13.4 years ago by
Sean Davis
21k • written 13.4 years ago by
adesh ashok
▴ 30
0
votes
1
reply
1.4k
views
Problem with addGeneIDs and org.Sc.sgd.db
Annotation
PROcess
Annotation
PROcess
updated 13.4 years ago by
Marc Carlson
★ 7.2k • written 13.5 years ago by
Susan Wilson
▴ 50
0
votes
5
replies
1.8k
views
Visualizing the region of classification uncertainty on thresholded images
PROcess
PROcess
updated 13.5 years ago by
Alex Gutteridge
▴ 650 • written 13.5 years ago by
Guest User
★ 13k
0
votes
1
reply
1.7k
views
biomaRt 'Please report this to the mailing list'
PROcess
biomaRt
PROcess
biomaRt
updated 13.5 years ago by
Sean Davis
21k • written 13.5 years ago by
John Coulthard
▴ 170
0
votes
1
reply
1.1k
views
edgeR- data for case studies
SAGE
PROcess
edgeR
SAGE
PROcess
edgeR
updated 13.5 years ago by
Johnson, Franklin Theodore
▴ 140 • written 13.5 years ago by
Gordon Smyth
53k
0
votes
0
replies
900
views
edgeR- data for case studies
PROcess
edgeR
PROcess
edgeR
13.5 years ago
Johnson, Franklin Theodore
▴ 140
0
votes
5
replies
3.0k
views
EasyRNASeq issue (missing bai files)
GO
PROcess
DESeq
easyRNASeq
GO
PROcess
DESeq
easyRNASeq
updated 13.5 years ago by
Jorge Beira
▴ 10 • written 13.5 years ago by
delhomme@embl.de
★ 1.2k
0
votes
0
replies
1.7k
views
SRAdb: differences between the database and the NCBI website
PROcess
SRAdb
PROcess
SRAdb
13.6 years ago
Ben Woodcroft
▴ 40
0
votes
0
replies
793
views
Illumnia Filtering
Sequencing
PROcess
Sequencing
PROcess
13.6 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
1
reply
1.3k
views
SWAN normalization for HumanMethylation450K - minfi
Normalization
PROcess
minfi
Normalization
PROcess
minfi
13.6 years ago
Lucia Lam
▴ 20
0
votes
0
replies
1.4k
views
miRNA exiqon panels and HTqPCR
miRNA
qPCR
PROcess
HTqPCR
miRNA
qPCR
PROcess
HTqPCR
13.6 years ago
Heidi Dvinge
★ 2.0k
0
votes
1
reply
2.4k
views
GEOquery, GSEMatrix parameter and lifecycle of GEO series data
GO
Biobase
PROcess
GEOquery
GO
Biobase
PROcess
GEOquery
updated 13.6 years ago by
Sean Davis
21k • written 13.6 years ago by
Gustavo Fernández Bayón
▴ 440
0
votes
3
replies
2.3k
views
GEOquery, GSEMatrix parameter and lifecycle of GEO series data
PROcess
GEOquery
PROcess
GEOquery
13.6 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
6
replies
1.7k
views
readGapppedAlignmentpairs questions
Coverage
PROcess
Coverage
PROcess
updated 13.6 years ago by
Wei Shi
★ 3.6k • written 13.6 years ago by
Lakshmanan Iyer
▴ 250
0
votes
0
replies
842
views
Coverage on GappedAlignment Pairs
Coverage
PROcess
Coverage
PROcess
13.6 years ago
Lakshmanan Iyer
▴ 50
0
votes
1
reply
1.3k
views
xps scheme building
Annotation
PROcess
xps
Annotation
PROcess
xps
updated 13.6 years ago by
cstrato
★ 3.9k • written 13.6 years ago by
Iain Gallagher
▴ 930
0
votes
3
replies
2.1k
views
Non-Specific Filtering with "nsFilter" Question
probe
genefilter
PROcess
probe
genefilter
PROcess
updated 13.6 years ago by
James W. MacDonald
68k • written 13.6 years ago by
zeynep özkeserli
▴ 160
0
votes
1
reply
1.2k
views
Problem in filtering of single color microarrray data using LIMMA
Microarray
Preprocessing
limma
PROcess
Microarray
Preprocessing
limma
PROcess
updated 13.6 years ago by
Belinda Phipson
▴ 130 • written 13.6 years ago by
Muralidharan V
▴ 60
0
votes
0
replies
1.4k
views
importing iScan data into beadarray
PROcess
beadarray
PROcess
beadarray
13.6 years ago
Craig Johnson
▴ 20
0
votes
0
replies
1.0k
views
pairwiseAlignment of PDB files to canonical protein structure
Alignment
Biostrings
PROcess
Alignment
Biostrings
PROcess
13.7 years ago
Gregory Ryslik
▴ 10
0
votes
6
replies
2.7k
views
error installing Rgraphviz
Rgraphviz
PROcess
BiocInstaller
Rgraphviz
PROcess
BiocInstaller
updated 13.7 years ago by
Dan Tenenbaum
★ 8.2k • written 13.7 years ago by
Mark Miller
▴ 10
0
votes
1
reply
1.4k
views
miRNA and other small RNAs
miRNA
Alignment
Annotation
PROcess
miRNA
Alignment
Annotation
PROcess
updated 13.7 years ago by
alessandro.guffanti@genomnia.com
▴ 330 • written 13.7 years ago by
Wu, Huiyun
▴ 70
0
votes
1
reply
1.7k
views
flowWorkspace transformation on FCS 3 data (Nikolas)
PROcess
flowWorkspace
PROcess
flowWorkspace
updated 13.8 years ago by
Nikolas
▴ 30 • written 13.8 years ago by
Greg Finak
▴ 240
0
votes
1
reply
2.0k
views
deprecated head file for RBGL and compilation failure
graph
RBGL
PROcess
graph
RBGL
PROcess
updated 13.8 years ago by
Vincent J. Carey, Jr.
6.7k • written 13.8 years ago by
Guest User
★ 13k
0
votes
0
replies
1.6k
views
Illumina beadarray analysis with lumi
Normalization
Preprocessing
probe
PROcess
beadarray
lumi
Normalization
Preprocessing
probe
13.8 years ago
Ahmet ZEHIR
▴ 50
0
votes
0
replies
1.7k
views
flowWorkspace transformation on FCS 3 data
PROcess
flowWorkspace
PROcess
flowWorkspace
13.8 years ago
Nikolas
▴ 30
0
votes
0
replies
1.0k
views
Can beadarray be use to analyze iScan raw data without perBeadFile.txt files?
PROcess
beadarray
PROcess
beadarray
13.8 years ago
Mike Smith
★ 6.6k
0
votes
1
reply
1.1k
views
Problems easyRNASeq
Annotation
PROcess
easyRNASeq
Annotation
PROcess
easyRNASeq
updated 13.8 years ago by
delhomme@embl.de
★ 1.2k • written 13.8 years ago by
Yates, Steven A
▴ 10
0
votes
1
reply
1.1k
views
Can beadarray be use to analyze iScan raw data without perBeadFile.txt files?
PROcess
beadarray
PROcess
beadarray
updated 13.8 years ago by
Mike Smith
★ 6.6k • written 13.8 years ago by
Guest User
★ 13k
0
votes
7
replies
2.2k
views
Install error affxparser for R 2.15
PROcess
affxparser
BiocInstaller
PROcess
affxparser
BiocInstaller
updated 13.8 years ago by
Dan Tenenbaum
★ 8.2k • written 13.8 years ago by
David Ruau
▴ 60
0
votes
0
replies
1.5k
views
JOB: Research Associate in Statistical Epigenomics (London)
Cancer
Ovarian
PROcess
Cancer
Ovarian
PROcess
13.9 years ago
Andrew Teschendorff
▴ 60
0
votes
1
reply
1.6k
views
Checking RNAseq DESeq pipeline
Sequencing
PROcess
DESeq
Sequencing
PROcess
DESeq
updated 13.9 years ago by
Wolfgang Huber
★ 13k • written 13.9 years ago by
nac
▴ 280
0
votes
1
reply
1.7k
views
FrozenRMA how to
Microarray
Network
hgu133plus2
Biobase
PROcess
KEGGSOAP
beadarray
EBImage
edgeR
frma
updated 13.9 years ago by
Matthew McCall
▴ 830 • written 13.9 years ago by
Alex Sanchez
▴ 20
0
votes
0
replies
2.1k
views
reading with lumi
Preprocessing
PROcess
lumi
methylumi
Preprocessing
PROcess
lumi
methylumi
13.9 years ago
Tim Triche
★ 4.2k
0
votes
3
replies
6.6k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 3.6 years ago by
pengmin.wang.1
• 0 • written 13.9 years ago by
Marc Carlson
★ 7.2k
0
votes
1
reply
1.2k
views
[R] tapply for enormous (>2^31 row) matrices
PROcess
PROcess
updated 13.9 years ago by
Gabor Grothendieck
▴ 30 • written 13.9 years ago by
Matthew Keller
▴ 100
651 results • Page
4 of 14
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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