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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.8 years ago by 53k • written 16.9 years ago by ▴ 30
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1.4k
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
4.2 years ago Shane • 0
0
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4
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21k
views
XML package cannot be installed
PROcess PROcess
updated 7.8 years ago by • 0 • written 13.5 years ago by ★ 13k
0
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8
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5.0k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.8 years ago by • 0 • written 12.0 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
8.5 years ago • updated 8.4 years ago bioDoctorate • 0
4
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8
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2.4k
views
Designing a model matrix and further process?
limma annotation R process
8.5 years ago Biotechuos4 • 0
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8
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2.9k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 8.8 years ago by ▴ 40 • written 19.4 years ago by ▴ 20
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8
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2.4k
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 9.1 years ago by • 0 • written 9.1 years ago by • 0
0
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1
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1.3k
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Error in reading file
process
updated 9.2 years ago by ★ 6.6k • written 9.2 years ago by • 0
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1.1k
views
Use of the GeneMeta package
process
9.3 years ago m.batzenschlager • 0
0
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0
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1.4k
views
about keeping the processing results in the computer memory
process
9.3 years ago Bogdan ▴ 670
0
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7
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3.3k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 9.4 years ago by • 0 • written 15.7 years ago by ★ 1.6k
2
votes
9
replies
4.3k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 9.8 years ago by 6.7k • written 11.7 years ago by 68k
0
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0
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1.5k
views
Help for affy
affy process probe
10.0 years ago weizhong_2007 • 0
0
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1
reply
1.6k
views
Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 10.3 years ago by • 0 • written 20.9 years ago by ▴ 320
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2
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 10.5 years ago by • 0 • written 11.8 years ago by ★ 13k
0
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6
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2.7k
views
is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 10.7 years ago by • 0 • written 13.0 years ago by ▴ 40
0
votes
2
replies
2.1k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.9 years ago by • 0 • written 21.3 years ago by ▴ 600
0
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1
reply
2.1k
views
Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 10.9 years ago by • 0 • written 14.5 years ago by ▴ 10
0
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1
reply
2.1k
views
MEDIPS quality control
process medips
updated 11.2 years ago by ▴ 570 • written 11.3 years ago by • 0
0
votes
1
reply
1.9k
views
champ package input
process
updated 11.3 years ago by 6.7k • written 11.3 years ago by • 0
1
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2
replies
6.5k
views
read .mat file in R
process
updated 11.3 years ago by ★ 3.0k • written 11.3 years ago by • 0
0
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1
reply
2.7k
views
Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 11.3 years ago by 1.6k • written 11.8 years ago by ★ 13k
0
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2
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5.1k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 11.4 years ago by ▴ 80 • written 11.4 years ago by ▴ 30
0
votes
1
reply
1.9k
views
Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 11.4 years ago by 21k • written 11.4 years ago by ▴ 20
0
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0
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2.7k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.5 years ago Bernd Fischer ▴ 550
0
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4
replies
2.8k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 11.5 years ago by 68k • written 11.5 years ago by ▴ 30
0
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2
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1.6k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 11.5 years ago by ★ 3.9k • written 11.5 years ago by ▴ 390
0
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6
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3.7k
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 11.5 years ago by 21k • written 11.5 years ago by ▴ 190
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2.7k
views
DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 11.5 years ago by 43k • written 11.5 years ago by ▴ 20
1
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1
reply
2.7k
views
How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 11.5 years ago by ★ 1.3k • written 11.5 years ago by ★ 13k
0
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0
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1.5k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
11.5 years ago Matthew McCall ▴ 830
0
votes
1
reply
1.6k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 90
0
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0
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1.5k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.6 years ago Brad Friedman ▴ 40
0
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1
reply
2.2k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 11.6 years ago by ★ 11k • written 11.6 years ago by ▴ 40
0
votes
2
replies
2.2k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 11.6 years ago by ▴ 20 • written 11.6 years ago by ★ 13k
0
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1
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1.6k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 11.6 years ago by 68k • written 11.6 years ago by ▴ 600
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0
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1.5k
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Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
11.6 years ago 张超 ▴ 50
0
votes
0
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1.9k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
11.7 years ago swarmqq@gmail.com ▴ 10
0
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0
replies
1.6k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
11.7 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.9k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
11.7 years ago Brian Herb ▴ 80
0
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0
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2.6k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
11.7 years ago Elena Serrano ▴ 30
0
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1
reply
4.1k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 13k
0
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0
replies
1.0k
views
strange spam from biocbuild
PROcess PROcess
11.8 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.3k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 11.8 years ago by 68k • written 11.8 years ago by ★ 13k
0
votes
5
replies
1.9k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 11.8 years ago by 68k • written 11.8 years ago by ▴ 110
0
votes
1
reply
2.3k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 11.8 years ago by 68k • written 11.8 years ago by ★ 13k
0
votes
0
replies
1.7k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
11.8 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
1.4k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
11.8 years ago James W. MacDonald 68k
0
votes
0
replies
1.9k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
11.8 years ago Rory Stark ★ 5.2k
651 results • Page 1 of 14
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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