Showing : process • reset
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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
4
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8
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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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deleted questions.. as its not very relevant..
process
6.8 years ago • updated 6.7 years ago bioDoctorate • 0
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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
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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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848
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Use of the GeneMeta package
process
7.6 years ago m.batzenschlager • 0
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about keeping the processing results in the computer memory
process
7.6 years ago Bogdan ▴ 670
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Help for affy
affy process probe
8.3 years ago weizhong_2007 • 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
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5.9k
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read .mat file in R
process
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
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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
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3.8k
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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
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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
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.8 years ago Bernd Fischer ▴ 550
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4
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2.2k
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.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
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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
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1
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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
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2.3k
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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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6
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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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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
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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
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.9 years ago Brad Friedman ▴ 40
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1.9k
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Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 40
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2
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1.8k
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xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ★ 13k
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1
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1.2k
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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
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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
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1.5k
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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
2
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9
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3.4k
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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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Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.0 years ago Kasper Daniel Hansen ★ 6.5k
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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
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Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
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1
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3.3k
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logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
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746
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strange spam from biocbuild
PROcess PROcess
10.1 years ago Marc Carlson ★ 7.2k
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1.0k
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help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
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5
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affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 10.1 years ago by 65k • written 10.1 years ago by ▴ 110
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1
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1.9k
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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
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0
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Factor-related problem when creating new flowFrame
PROcess PROcess
10.1 years ago Kipper Fletez-Brant ▴ 150
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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
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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
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data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
10.1 years ago Rory Stark ★ 5.2k
0
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1
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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
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3
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1.3k
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recommend package for exon array analysis
PROcess PROcess
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ★ 13k
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GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
10.2 years ago Dale Richardson ▴ 30
0
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1
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1.3k
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VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
vsn PROcess xps vsn PROcess xps
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 350
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894
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question regarding function IMA.methy450PP in IMA package
PROcess PROcess
10.2 years ago Jack Luo ▴ 440
0
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12
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3.0k
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bumphunter DMRs difficulties
PROcess minfi bumphunter PROcess minfi bumphunter
updated 10.2 years ago by ★ 6.5k • written 10.2 years ago by ▴ 160
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votes
2
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2.3k
views
Limma design : What is the "best" method to infer biological replicates during differentially expression analysis
Microarray limma PROcess Microarray limma PROcess
updated 10.2 years ago by 50k • written 10.2 years ago by ▴ 20
1
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3
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1.5k
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RMA on Exon Array NaN values
Normalization PROcess Normalization PROcess
updated 10.2 years ago by ★ 4.3k • written 10.2 years ago by ▴ 40
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votes
2
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1.3k
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Tigre Package question 3
Microarray impute PROcess convert mmgmos puma tigre trigger Microarray impute PROcess
updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 50
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0
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973
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FW: Tigre Package question 3
impute PROcess mmgmos puma impute PROcess mmgmos puma
10.2 years ago Solanki, Anisha ▴ 60
50 results • Page 1 of 1
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Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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