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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 17 months ago by 48k • written 14.6 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
22 months ago Shane • 0
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4
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XML package cannot be installed
PROcess PROcess
updated 5.5 years ago by • 0 • written 11.2 years ago by ★ 12k
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8
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3.5k
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error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 5.5 years ago by • 0 • written 9.6 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
6.2 years ago • updated 6.1 years ago bioDoctorate • 0
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8
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1.6k
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Designing a model matrix and further process?
limma annotation R process
6.2 years ago Biotechuos4 • 0
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8
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1.6k
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raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 6.5 years ago by ▴ 40 • written 17.1 years ago by ▴ 20
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8
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1.5k
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 6.8 years ago by • 0 • written 6.8 years ago by • 0
0
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846
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Error in reading file
process
updated 6.9 years ago by ★ 6.1k • written 6.9 years ago by • 0
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732
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Use of the GeneMeta package
process
7.0 years ago m.batzenschlager • 0
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908
views
about keeping the processing results in the computer memory
process
7.0 years ago Bogdan ▴ 660
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7
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1.9k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.1 years ago by • 0 • written 13.4 years ago by 1.6k
2
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9
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3.1k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 7.5 years ago by 6.7k • written 9.4 years ago by 63k
0
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0
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1.0k
views
Help for affy
affy process probe
7.7 years ago weizhong_2007 • 0
0
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1
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1.0k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 8.0 years ago by • 0 • written 18.6 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 8.1 years ago by • 0 • written 9.5 years ago by ★ 12k
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6
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1.7k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 8.4 years ago by • 0 • written 10.7 years ago by ▴ 40
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2
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1.4k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 8.6 years ago by • 0 • written 19.0 years ago by ▴ 600
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1
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1.5k
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 8.6 years ago by • 0 • written 12.2 years ago by ▴ 10
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1
reply
1.5k
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MEDIPS quality control
process medips
updated 8.9 years ago by ▴ 570 • written 9.0 years ago by • 0
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1
reply
1.4k
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champ package input
process
updated 8.9 years ago by 6.7k • written 9.0 years ago by • 0
1
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2
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read .mat file in R
process
updated 9.0 years ago by ★ 2.8k • written 9.0 years ago by • 0
0
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1
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1.4k
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Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 9.0 years ago by 1.6k • written 9.5 years ago by ★ 12k
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2
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3.5k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 9.1 years ago by ▴ 80 • written 9.1 years ago by ▴ 30
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1
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1.3k
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Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 9.1 years ago by 21k • written 9.1 years ago by ▴ 20
0
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0
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2.1k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.2 years ago Bernd Fischer ▴ 550
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4
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2.0k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 9.2 years ago by 63k • written 9.2 years ago by ▴ 30
0
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2
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1.1k
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xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 9.2 years ago by ★ 3.9k • written 9.2 years ago by ▴ 350
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6
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2.6k
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 9.2 years ago by 21k • written 9.2 years ago by ▴ 190
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2.1k
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DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 9.2 years ago by 40k • written 9.2 years ago by ▴ 20
1
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1
reply
2.1k
views
How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ★ 12k
0
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0
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1.1k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
9.2 years ago Matthew McCall ▴ 830
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1
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1.2k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 90
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1.0k
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.3 years ago Brad Friedman ▴ 40
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1
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1.7k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 9.3 years ago by 11k • written 9.3 years ago by ▴ 40
0
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2
replies
1.6k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 9.3 years ago by ▴ 20 • written 9.3 years ago by ★ 12k
0
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1
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1.1k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 9.3 years ago by 63k • written 9.3 years ago by ▴ 590
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views
Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
9.3 years ago 张超 ▴ 50
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0
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1.3k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
9.3 years ago swarmqq@gmail.com ▴ 10
0
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1.1k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
9.4 years ago Kasper Daniel Hansen 6.5k
0
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0
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1.4k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
9.4 years ago Brian Herb ▴ 80
0
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0
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1.9k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
9.4 years ago Elena Serrano ▴ 30
0
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1
reply
3.0k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 9.4 years ago by 13k • written 9.4 years ago by ★ 12k
0
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0
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628
views
strange spam from biocbuild
PROcess PROcess
9.4 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
890
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 9.4 years ago by 63k • written 9.4 years ago by ★ 12k
0
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5
replies
1.3k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 9.5 years ago by 63k • written 9.5 years ago by ▴ 110
0
votes
1
reply
1.7k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 9.5 years ago by 63k • written 9.5 years ago by ★ 12k
0
votes
0
replies
1.2k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
9.5 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
911
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
9.5 years ago James W. MacDonald 63k
0
votes
0
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1.4k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
9.5 years ago Rory Stark ★ 5.0k
50 results • Page 1 of 1
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Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Answer: ''Model_Matrix'' error by Gordon Smyth 48k
This is actually an error message from base R rather than from limma. The error says that `Group` contains 0 or 1 levels, so your assumptio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
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