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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.4 years ago by 53k • written 16.5 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
3.8 years ago Shane • 0
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4
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XML package cannot be installed
PROcess PROcess
updated 7.4 years ago by • 0 • written 13.1 years ago by ★ 13k
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8
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error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.5 years ago by • 0 • written 11.6 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
8.2 years ago • updated 8.1 years ago bioDoctorate • 0
4
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8
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Designing a model matrix and further process?
limma annotation R process
8.1 years ago Biotechuos4 • 0
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2.6k
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raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 8.5 years ago by ▴ 40 • written 19.0 years ago by ▴ 20
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8
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 8.8 years ago by • 0 • written 8.8 years ago by • 0
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1.2k
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Error in reading file
process
updated 8.9 years ago by ★ 6.6k • written 8.9 years ago by • 0
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1.0k
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Use of the GeneMeta package
process
8.9 years ago m.batzenschlager • 0
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about keeping the processing results in the computer memory
process
9.0 years ago Bogdan ▴ 670
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7
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2.9k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 9.1 years ago by • 0 • written 15.4 years ago by ★ 1.6k
2
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9
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GEOquery error
Annotation PROcess Annotation PROcess
updated 9.5 years ago by 6.7k • written 11.4 years ago by 68k
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1.4k
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Help for affy
affy process probe
9.6 years ago weizhong_2007 • 0
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1
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1.5k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 10.0 years ago by • 0 • written 20.6 years ago by ▴ 320
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 10.1 years ago by • 0 • written 11.5 years ago by ★ 13k
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6
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2.5k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 10.4 years ago by • 0 • written 12.6 years ago by ▴ 40
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2
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2.0k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.5 years ago by • 0 • written 21.0 years ago by ▴ 600
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 10.5 years ago by • 0 • written 14.1 years ago by ▴ 10
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1
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2.0k
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MEDIPS quality control
process medips
updated 10.9 years ago by ▴ 570 • written 11.0 years ago by • 0
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1
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champ package input
process
updated 10.9 years ago by 6.7k • written 10.9 years ago by • 0
1
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2
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read .mat file in R
process
updated 10.9 years ago by ★ 3.0k • written 10.9 years ago by • 0
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2.5k
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Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 11.0 years ago by 1.6k • written 11.5 years ago by ★ 13k
0
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2
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4.8k
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getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 11.1 years ago by ▴ 80 • written 11.1 years ago by ▴ 30
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1
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1.8k
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Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 11.1 years ago by 21k • written 11.1 years ago by ▴ 20
0
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.1 years ago Bernd Fischer ▴ 550
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4
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2.7k
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.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 30
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2
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xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 11.1 years ago by ★ 3.9k • written 11.2 years ago by ▴ 380
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6
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 11.2 years ago by 21k • written 11.2 years ago by ▴ 190
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DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 11.2 years ago by 43k • written 11.2 years ago by ▴ 20
1
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1
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2.6k
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How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 11.2 years ago by ★ 1.3k • written 11.2 years ago by ★ 13k
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R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
11.2 years ago Matthew McCall ▴ 830
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1
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1.6k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 11.2 years ago by 16k • written 11.2 years ago by ▴ 90
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.2 years ago Brad Friedman ▴ 40
0
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1
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2.1k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 11.2 years ago by ★ 11k • written 11.2 years ago by ▴ 40
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2
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2.1k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 11.3 years ago by ▴ 20 • written 11.3 years ago by ★ 13k
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1
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1.5k
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Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 11.3 years ago by 68k • written 11.3 years ago by ▴ 600
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Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
11.3 years ago 张超 ▴ 50
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0
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1.8k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
11.3 years ago swarmqq@gmail.com ▴ 10
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1.5k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
11.4 years ago Kasper Daniel Hansen ★ 6.5k
0
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1.8k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
11.4 years ago Brian Herb ▴ 80
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2.5k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
11.4 years ago Elena Serrano ▴ 30
0
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1
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4.0k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 11.4 years ago by ★ 13k • written 11.4 years ago by ★ 13k
0
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0
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950
views
strange spam from biocbuild
PROcess PROcess
11.4 years ago Marc Carlson ★ 7.2k
0
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1
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1.2k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 11.4 years ago by 68k • written 11.4 years ago by ★ 13k
0
votes
5
replies
1.8k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 11.4 years ago by 68k • written 11.4 years ago by ▴ 110
0
votes
1
reply
2.2k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 11.4 years ago by 68k • written 11.4 years ago by ★ 13k
0
votes
0
replies
1.6k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
11.4 years ago Kipper Fletez-Brant ▴ 150
0
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0
replies
1.3k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
11.5 years ago James W. MacDonald 68k
0
votes
0
replies
1.8k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
11.5 years ago Rory Stark ★ 5.2k
651 results • Page 1 of 14
Recent ...
Replies
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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