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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 2.1 years ago by 50k • written 15.2 years ago by ▴ 30
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.5 years ago Shane • 0
0
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4
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XML package cannot be installed
PROcess PROcess
updated 6.1 years ago by • 0 • written 11.8 years ago by ★ 13k
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8
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4.0k
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error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 6.1 years ago by • 0 • written 10.3 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
6.8 years ago • updated 6.7 years ago bioDoctorate • 0
4
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8
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1.8k
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Designing a model matrix and further process?
limma annotation R process
6.8 years ago Biotechuos4 • 0
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8
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1.9k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 7.1 years ago by ▴ 40 • written 17.7 years ago by ▴ 20
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8
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1.8k
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 7.4 years ago by • 0 • written 7.4 years ago by • 0
0
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1
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973
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Error in reading file
process
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by • 0
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0
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848
views
Use of the GeneMeta package
process
7.6 years ago m.batzenschlager • 0
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0
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1.1k
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about keeping the processing results in the computer memory
process
7.6 years ago Bogdan ▴ 670
0
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7
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2.2k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.7 years ago by • 0 • written 14.1 years ago by ★ 1.6k
2
votes
9
replies
3.4k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 8.2 years ago by 6.7k • written 10.0 years ago by 65k
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0
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1.2k
views
Help for affy
affy process probe
8.3 years ago weizhong_2007 • 0
0
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1
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1.2k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 8.7 years ago by • 0 • written 19.2 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 8.8 years ago by • 0 • written 10.1 years ago by ★ 13k
0
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6
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2.0k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 9.0 years ago by • 0 • written 11.3 years ago by ▴ 40
0
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2
replies
1.6k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 9.2 years ago by • 0 • written 19.6 years ago by ▴ 600
0
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1
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1.7k
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 9.2 years ago by • 0 • written 12.8 years ago by ▴ 10
0
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1
reply
1.7k
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MEDIPS quality control
process medips
updated 9.5 years ago by ▴ 570 • written 9.6 years ago by • 0
0
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1
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1.6k
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champ package input
process
updated 9.6 years ago by 6.7k • written 9.6 years ago by • 0
1
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2
replies
5.9k
views
read .mat file in R
process
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
0
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1
reply
1.8k
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Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 9.6 years ago by 1.6k • written 10.1 years ago by ★ 13k
0
votes
2
replies
3.9k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 9.7 years ago by ▴ 80 • written 9.7 years ago by ▴ 30
0
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1
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1.5k
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Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 9.7 years ago by 21k • written 9.7 years ago by ▴ 20
0
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0
replies
2.3k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.8 years ago Bernd Fischer ▴ 550
0
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4
replies
2.2k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 30
0
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2
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1.2k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 9.8 years ago by ★ 3.9k • written 9.8 years ago by ▴ 350
0
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6
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3.0k
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 9.8 years ago by 21k • written 9.8 years ago by ▴ 190
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2.3k
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DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 9.8 years ago by 42k • written 9.8 years ago by ▴ 20
1
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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 ★ 1.3k • written 9.8 years ago by ★ 13k
0
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0
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1.2k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
9.9 years ago Matthew McCall ▴ 830
0
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1
reply
1.3k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 90
0
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0
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1.2k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.9 years ago Brad Friedman ▴ 40
0
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1
reply
1.9k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 40
0
votes
2
replies
1.8k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ★ 13k
0
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1
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1.2k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 590
0
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0
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1.2k
views
Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
9.9 years ago 张超 ▴ 50
0
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0
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1.5k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.0 years ago swarmqq@gmail.com ▴ 10
0
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0
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1.3k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.0 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
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1.5k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
10.0 years ago Brian Herb ▴ 80
0
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0
replies
2.1k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
0
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1
reply
3.3k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
0
votes
0
replies
746
views
strange spam from biocbuild
PROcess PROcess
10.1 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.0k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
0
votes
5
replies
1.5k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 10.1 years ago by 65k • written 10.1 years ago by ▴ 110
0
votes
1
reply
1.9k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
10.1 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
1.1k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
10.1 years ago James W. MacDonald 65k
0
votes
0
replies
1.6k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
10.1 years ago Rory Stark ★ 5.2k
50 results • Page 1 of 1
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Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
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Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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