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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 2.7 years ago by 52k • written 15.8 years ago by ▴ 30
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1.0k
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
3.0 years ago Shane • 0
0
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4
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20k
views
XML package cannot be installed
PROcess PROcess
updated 6.7 years ago by • 0 • written 12.4 years ago by ★ 13k
0
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8
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4.4k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 6.7 years ago by • 0 • written 10.8 years ago by ▴ 300
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1.2k
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deleted questions.. as its not very relevant..
process
7.4 years ago • updated 7.3 years ago bioDoctorate • 0
4
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8
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2.0k
views
Designing a model matrix and further process?
limma annotation R process
7.4 years ago Biotechuos4 • 0
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8
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2.2k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 7.7 years ago by ▴ 40 • written 18.2 years ago by ▴ 20
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8
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2.0k
views
`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 8.0 years ago by • 0 • written 8.0 years ago by • 0
0
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1
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1.1k
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Error in reading file
process
updated 8.1 years ago by ★ 6.6k • written 8.1 years ago by • 0
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943
views
Use of the GeneMeta package
process
8.1 years ago m.batzenschlager • 0
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0
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1.2k
views
about keeping the processing results in the computer memory
process
8.2 years ago Bogdan ▴ 670
0
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7
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2.5k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 8.3 years ago by • 0 • written 14.6 years ago by ★ 1.6k
2
votes
9
replies
3.7k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 8.7 years ago by 6.7k • written 10.6 years ago by 67k
0
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0
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1.3k
views
Help for affy
affy process probe
8.8 years ago weizhong_2007 • 0
0
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1
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1.3k
views
Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 9.2 years ago by • 0 • written 19.8 years ago by ▴ 320
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2
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1.9k
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 9.3 years ago by • 0 • written 10.7 years ago by ★ 13k
0
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6
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2.2k
views
is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 9.6 years ago by • 0 • written 11.9 years ago by ▴ 40
0
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2
replies
1.8k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 9.7 years ago by • 0 • written 20.2 years ago by ▴ 600
0
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1
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1.8k
views
Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 9.7 years ago by • 0 • written 13.4 years ago by ▴ 10
0
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1
reply
1.9k
views
MEDIPS quality control
process medips
updated 10.1 years ago by ▴ 570 • written 10.2 years ago by • 0
0
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1
reply
1.7k
views
champ package input
process
updated 10.1 years ago by 6.7k • written 10.1 years ago by • 0
1
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2
replies
6.1k
views
read .mat file in R
process
updated 10.2 years ago by ★ 3.0k • written 10.2 years ago by • 0
0
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1
reply
2.1k
views
Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 10.2 years ago by 1.6k • written 10.7 years ago by ★ 13k
0
votes
2
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4.2k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 10.3 years ago by ▴ 80 • written 10.3 years ago by ▴ 30
0
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1
reply
1.7k
views
Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 10.3 years ago by 21k • written 10.3 years ago by ▴ 20
0
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0
replies
2.5k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
10.3 years ago Bernd Fischer ▴ 550
0
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4
replies
2.5k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 10.4 years ago by 67k • written 10.4 years ago by ▴ 30
0
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2
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1.4k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 10.4 years ago by ★ 3.9k • written 10.4 years ago by ▴ 380
0
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6
replies
3.2k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 10.4 years ago by 21k • written 10.4 years ago by ▴ 190
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2.5k
views
DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 20
1
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1
reply
2.5k
views
How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 10.4 years ago by ★ 1.3k • written 10.4 years ago by ★ 13k
0
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0
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1.4k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
10.4 years ago Matthew McCall ▴ 830
0
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1
reply
1.4k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 90
0
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0
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1.3k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
10.4 years ago Brad Friedman ▴ 40
0
votes
1
reply
2.0k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 10.5 years ago by ★ 11k • written 10.5 years ago by ▴ 40
0
votes
2
replies
2.0k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 10.5 years ago by ▴ 20 • written 10.5 years ago by ★ 13k
0
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1
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1.4k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 10.5 years ago by 67k • written 10.5 years ago by ▴ 600
0
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0
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1.3k
views
Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
10.5 years ago 张超 ▴ 50
0
votes
0
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1.6k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.5 years ago swarmqq@gmail.com ▴ 10
0
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0
replies
1.4k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.6 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.7k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
10.6 years ago Brian Herb ▴ 80
0
votes
0
replies
2.3k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.6 years ago Elena Serrano ▴ 30
0
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1
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3.6k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ★ 13k
0
votes
0
replies
835
views
strange spam from biocbuild
PROcess PROcess
10.6 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.1k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.6 years ago by 67k • written 10.6 years ago by ★ 13k
0
votes
5
replies
1.6k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 10.7 years ago by 67k • written 10.7 years ago by ▴ 110
0
votes
1
reply
2.1k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 10.7 years ago by 67k • written 10.7 years ago by ★ 13k
0
votes
0
replies
1.5k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
10.7 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
1.2k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
10.7 years ago James W. MacDonald 67k
0
votes
0
replies
1.7k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
10.7 years ago Rory Stark ★ 5.2k
50 results • Page 1 of 1
Recent ...
Replies
Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.
Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k
Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.
Comment: Differential Expression Genes as Independent Variables by abadgerw • 0
The data that is repeated is a quantitative metric of post-mortem pathology across multiple sections. Not all patients have the same number…
Answer: Crossover design with limma by Gordon Smyth 52k
Your experiment is somewhat more elaborate than a classical crossover design because of the period-specific baseline controls. The analyses…
Answer: Differential Expression Genes as Independent Variables by Gordon Smyth 52k
Sorry, your question doesn't make sense to me. There are tens of thousands of genes and you can't run a mixed model analysis with one depen…
Votes
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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