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Showing :
process
•
reset
4
votes
8
replies
1.8k
views
Designing a model matrix and further process?
limma
annotation
R
process
6.8 years ago
Biotechuos4
• 0
3
votes
3
replies
1.3k
views
EBImage: filtering in the presence of NAs
PROcess
EBImage
PROcess
EBImage
updated 11.1 years ago by
Wolfgang Huber
★ 13k • written 11.1 years ago by
Arnaud Duranel
▴ 60
2
votes
6
replies
9.5k
views
GEOquery: how to extract experimental data? (confused)
PROcess
GEOquery
PROcess
GEOquery
updated 12.7 years ago by
Dai, Hongying,
▴ 60 • written 12.7 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k
2
votes
3
replies
2.1k
views
How to get position for each gene ID/gene symbol instead of position for each transcript
Organism
PROcess
biomaRt
GenomicFeatures
Organism
PROcess
biomaRt
GenomicFeatures
updated 13.7 years ago by
Steve Lianoglou
★ 13k • written 13.7 years ago by
shirley zhang
★ 1.0k
2
votes
4
replies
6.3k
views
Too many (?) differentially expressed genes - edgeR and DESeq
PROcess
edgeR
DESeq
PROcess
edgeR
DESeq
updated 10.8 years ago by
Wolfgang Huber
★ 13k • written 10.8 years ago by
Darya Vanichkina
▴ 120
2
votes
9
replies
3.4k
views
GEOquery error
Annotation
PROcess
Annotation
PROcess
updated 8.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.0 years ago by
James W. MacDonald
65k
1
vote
1
reply
2.3k
views
How to hide or suppress note about ward method in clValid package?
Annotation
PROcess
Annotation
PROcess
updated 9.8 years ago by
Julian Gehring
★ 1.3k • written 9.8 years ago by
Guest User
★ 13k
1
vote
2
replies
5.8k
views
read .mat file in R
process
updated 9.6 years ago by
Peter Langfelder
★ 3.0k • written 9.6 years ago by
s.kazemi.n
• 0
1
vote
3
replies
1.5k
views
RMA on Exon Array NaN values
Normalization
PROcess
Normalization
PROcess
updated 10.2 years ago by
Benilton Carvalho
★ 4.3k • written 10.2 years ago by
Nicolas Servant
▴ 40
1
vote
2
replies
1.0k
views
deleted questions.. as its not very relevant..
process
6.8 years ago • updated 6.7 years ago
bioDoctorate
• 0
1
vote
9
replies
2.8k
views
BLAST search sequence for species ID from R?
Biostrings
PROcess
Biostrings
PROcess
updated 14.4 years ago by
Michael Dondrup
▴ 550 • written 14.4 years ago by
jos matejus
▴ 40
1
vote
0
replies
761
views
GSEA with one class metaanalysis
PROcess
PROcess
17.2 years ago
Gordon Smyth
50k
1
vote
0
replies
878
views
RmiR, request for new package
miRNA
Annotation
GO
cdf
probe
PROcess
Category
miRNA
Annotation
GO
cdf
probe
PROcess
15.2 years ago
Nishant Gopalakrishnan
▴ 340
0
votes
0
replies
1.7k
views
getSeq human genomic sequences
Annotation
Cancer
BSgenome
PROcess
GLAD
BSgenome
IRanges
Annotation
Cancer
BSgenome
GLAD
15.2 years ago
Hervé Pagès
16k
0
votes
1
reply
2.8k
views
BIRD 2008
Genetics
Pathways
Cancer
PROcess
microRNA
a4
Genetics
Pathways
Cancer
PROcess
microRNA
16.5 years ago
Prof. Roland Wagner
▴ 100
0
votes
0
replies
840
views
ABPkgBuilder Error; Again
Annotation
GO
Cancer
Organism
Biobase
annotate
AnnBuilder
PROcess
Annotation
GO
Cancer
18.7 years ago
Barry Henderson
▴ 250
0
votes
4
replies
2.1k
views
disagreement between biomaRt and topGO
GO
hgu133plus2
annotate
geneplotter
graph
Rgraphviz
PROcess
goTools
biomaRt
Category
GO
updated 16.6 years ago by
Steffen
▴ 500 • written 16.7 years ago by
Dick Beyer
★ 1.4k
0
votes
0
replies
762
views
dChip v li.wong() (Was: Re: warnings from li wong summary method in expresso)
Microarray
Normalization
Preprocessing
Cancer
hgu133plus2
probe
affy
limma
PROcess
Cancer
17.2 years ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
968
views
FW: makecdfenv()
GO
cdf
PROcess
altcdfenvs
GO
cdf
PROcess
altcdfenvs
19.8 years ago
Lana Schaffer
▴ 80
0
votes
0
replies
748
views
Re: [R] Source package installation for WinXPpro
Microarray
Cancer
affy
PROcess
Microarray
Cancer
affy
PROcess
20.6 years ago
James W. MacDonald
65k
0
votes
2
replies
1.2k
views
affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Microarray
cdf
affy
makecdfenv
PROcess
oligo
cycle
Microarray
cdf
affy
makecdfenv
oligo
updated 12.3 years ago by
James W. MacDonald
65k • written 12.3 years ago by
Groot, Philip de
▴ 630
0
votes
1
reply
1.5k
views
Summarising Probe Sets for Agilent 4x44 Arrays
Clustering
probe
PROcess
Clustering
probe
PROcess
updated 12.4 years ago by
Francois Pepin
▴ 80 • written 12.4 years ago by
Samantha Jane England
▴ 10
0
votes
4
replies
1.4k
views
use of duplicateCorrelation in Limma with agilent one-color arrays
limma
PROcess
limma
PROcess
updated 12.2 years ago by
Gordon Smyth
50k • written 12.2 years ago by
Jabez Wilson
▴ 150
0
votes
1
reply
1.3k
views
flowWorkspace transformation on FCS 3 data (Nikolas)
PROcess
flowWorkspace
PROcess
flowWorkspace
updated 12.0 years ago by
Nikolas
▴ 30 • written 12.0 years ago by
Greg Finak
▴ 240
0
votes
5
replies
2.4k
views
EasyRNASeq issue (missing bai files)
GO
PROcess
DESeq
easyRNASeq
GO
PROcess
DESeq
easyRNASeq
updated 11.8 years ago by
Jorge Beira
▴ 10 • written 11.8 years ago by
delhomme@embl.de
★ 1.2k
0
votes
5
replies
1.3k
views
Visualizing the region of classification uncertainty on thresholded images
PROcess
PROcess
updated 11.7 years ago by
Alex Gutteridge
▴ 650 • written 11.7 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
Fwd: ASSIST on contrast matrix
Network
Homo sapiens
limma
PROcess
Network
Homo sapiens
limma
PROcess
11.7 years ago
Seyed Ahmad Mousavi
▴ 10
0
votes
0
replies
1.5k
views
Classification in Mass Spectrometry Data
Microarray
Classification
Cancer
Ovarian
PROcess
MLInterfaces
ASSIGN
Microarray
Cancer
11.5 years ago
McGee, Monnie
▴ 300
0
votes
3
replies
3.0k
views
Subsetting expression sets for mass spec data - second ask
Classification
Cancer
PROcess
Classification
Cancer
PROcess
updated 11.4 years ago by
Sean Davis
21k • written 11.4 years ago by
McGee, Monnie
▴ 300
0
votes
7
replies
3.6k
views
Weird things happening with minfi and RcppEigen
PROcess
minfi
PROcess
minfi
updated 11.4 years ago by
Benilton Carvalho
★ 4.3k • written 11.4 years ago by
Gustavo Fernández Bayón
▴ 440
0
votes
0
replies
936
views
FDA soliciting proposals to analyze gene expression datasets
Microarray
Pharmacogenomics
PROcess
Microarray
Pharmacogenomics
PROcess
18.0 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
1.2k
views
cghMCR package:Is it possible to find MCR by not usingDNAcopy object?
PROcess
DNAcopy
cghMCR
PROcess
DNAcopy
cghMCR
12.6 years ago
viritha kaza
▴ 580
0
votes
0
replies
989
views
FW: normalization one color microarrays
Normalization
hgug4112a
PROcess
Agi4x44PreProcess
Normalization
hgug4112a
PROcess
12.7 years ago
Paz Tapia Ramirez
▴ 150
0
votes
1
reply
1.1k
views
Issues with BioC GO annotations and NetAffx
Annotation
GO
probe
affy
PROcess
GOstats
Category
Annotation
GO
probe
affy
PROcess
updated 18.1 years ago by
Seth Falcon
★ 7.4k • written 18.1 years ago by
Bornman, Daniel M
▴ 110
0
votes
4
replies
1.1k
views
win 64bit and general BioC computing power?
GO
Clustering
affy
limma
gcrma
PROcess
GO
Clustering
affy
limma
gcrma
PROcess
updated 19.9 years ago by
Liaw, Andy
▴ 360 • written 19.9 years ago by
Matthew Hannah
▴ 940
0
votes
0
replies
1.2k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO
probe
PROcess
frma
GO
probe
PROcess
frma
9.8 years ago
Matthew McCall
▴ 830
0
votes
2
replies
1.7k
views
preparing sequencing data for use with anota
Sequencing
Normalization
PROcess
anota
Sequencing
Normalization
PROcess
anota
updated 8.7 years ago by
kesarwani.anil
• 0 • written 10.1 years ago by
Guest User
★ 13k
0
votes
0
replies
1.0k
views
Question about 'updateCel' from package 'affxparser'
cdf
PROcess
affxparser
cdf
PROcess
affxparser
12.7 years ago
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
955
views
Affymetrix exon arrays?
Normalization
Cancer
Breast
cdf
affy
PROcess
Normalization
Cancer
Breast
cdf
affy
updated 17.6 years ago by
Jesse Salisbury
▴ 20 • written 17.6 years ago by
Steven McKinney
▴ 310
0
votes
4
replies
1.9k
views
peer review process for bioconductor packages
PROcess
PROcess
22.1 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
0
replies
1.0k
views
(1) Anova for 12 Affy yeast chips (Yg98) // (2) Problem fitting Li&Wong model with Affy 1.0 :
GO
Yeast
cdf
genefilter
affy
PROcess
GO
Yeast
cdf
genefilter
affy
PROcess
22.0 years ago
julien.sylvestre@wotan.ens.fr
▴ 50
0
votes
2
replies
1.3k
views
affy expression values
Proteomics
affy
PROcess
Proteomics
affy
PROcess
updated 21.8 years ago by
Rafael A. Irizarry
▴ 640 • written 21.8 years ago by
Larry
▴ 10
0
votes
1
reply
1.0k
views
Annotation for Nonspecificity of Affymetrix Probes?
probe
PROcess
probe
PROcess
updated 21.7 years ago by
rgentleman
★ 5.5k • written 21.7 years ago by
Jeff Sorenson
▴ 70
0
votes
1
reply
986
views
Problem whit Affy
GO
cdf
probe
PROcess
GO
cdf
probe
PROcess
updated 21.6 years ago by
Rafael A. Irizarry
▴ 640 • written 21.6 years ago by
Remo Sanges
▴ 10
0
votes
6
replies
1.3k
views
request for letter of support
PROcess
PROcess
updated 21.5 years ago by
Hinnerk Boriss
▴ 220 • written 21.5 years ago by
rgentleman
★ 5.5k
0
votes
1
reply
1.3k
views
Job Posting in Biostatistics/Statistics
Bayesian
Survival
Cancer
PROcess
ASSET
Bayesian
Survival
Cancer
PROcess
ASSET
updated 21.4 years ago by
Johannes Hüsing
▴ 80 • written 21.4 years ago by
Janusz Kawczak
▴ 10
0
votes
0
replies
775
views
protien and peptide mass spectrometry
genefilter
PROcess
genefilter
PROcess
21.3 years ago
Nicholas Lewin-Koh
▴ 430
0
votes
0
replies
584
views
Widget option enabled:Thank you
PROcess
PROcess
21.3 years ago
Tapan Mehta
▴ 270
0
votes
0
replies
1.3k
views
InfoVis 2003 Call for Papers
Visualization
PROcess
Category
Visualization
PROcess
Category
21.2 years ago
rgentleman
★ 5.5k
0
votes
3
replies
2.2k
views
Getting GO ids for genenames in plasmodium falciparum
GO
Plasmodium falciparum
PROcess
convert
GO
Plasmodium falciparum
PROcess
convert
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
Guest User
★ 13k
50 results • Page
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Replies
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…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
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)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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