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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.0 years ago by 52k • written 16.1 years ago by ▴ 30
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1.1k
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
3.4 years ago Shane • 0
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4
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20k
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XML package cannot be installed
PROcess PROcess
updated 7.0 years ago by • 0 • written 12.7 years ago by ★ 13k
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8
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4.6k
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error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.0 years ago by • 0 • written 11.1 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
7.7 years ago • updated 7.6 years ago bioDoctorate • 0
4
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8
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2.1k
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Designing a model matrix and further process?
limma annotation R process
7.7 years ago Biotechuos4 • 0
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8
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2.3k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 8.0 years ago by ▴ 40 • written 18.6 years ago by ▴ 20
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8
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2.1k
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 8.3 years ago by • 0 • written 8.3 years ago by • 0
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1
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1.1k
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Error in reading file
process
updated 8.4 years ago by ★ 6.6k • written 8.4 years ago by • 0
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973
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Use of the GeneMeta package
process
8.5 years ago m.batzenschlager • 0
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0
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1.2k
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about keeping the processing results in the computer memory
process
8.5 years ago Bogdan ▴ 670
0
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7
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2.7k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 8.6 years ago by • 0 • written 14.9 years ago by ★ 1.6k
2
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9
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GEOquery error
Annotation PROcess Annotation PROcess
updated 9.0 years ago by 6.7k • written 10.9 years ago by 68k
0
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0
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1.3k
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Help for affy
affy process probe
9.2 years ago weizhong_2007 • 0
0
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1
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1.4k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 9.5 years ago by • 0 • written 20.1 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 9.6 years ago by • 0 • written 11.0 years ago by ★ 13k
0
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6
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2.3k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 9.9 years ago by • 0 • written 12.2 years ago by ▴ 40
0
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2
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1.9k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.1 years ago by • 0 • written 20.5 years ago by ▴ 600
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1
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1.9k
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 10.1 years ago by • 0 • written 13.7 years ago by ▴ 10
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1
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1.9k
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MEDIPS quality control
process medips
updated 10.4 years ago by ▴ 570 • written 10.5 years ago by • 0
0
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1
reply
1.8k
views
champ package input
process
updated 10.4 years ago by 6.7k • written 10.4 years ago by • 0
1
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2
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6.2k
views
read .mat file in R
process
updated 10.5 years ago by ★ 3.0k • written 10.5 years ago by • 0
0
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1
reply
2.3k
views
Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 10.5 years ago by 1.6k • written 11.0 years ago by ★ 13k
0
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2
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4.5k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 10.6 years ago by ▴ 80 • written 10.6 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 10.6 years ago by 21k • written 10.6 years ago by ▴ 20
0
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0
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2.5k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
10.7 years ago Bernd Fischer ▴ 550
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4
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2.5k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 10.7 years ago by 68k • written 10.7 years ago by ▴ 30
0
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2
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1.5k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 10.7 years ago by ★ 3.9k • written 10.7 years ago by ▴ 380
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6
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3.3k
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 10.7 years ago by 21k • written 10.7 years ago by ▴ 190
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2.6k
views
DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 20
1
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1
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2.6k
views
How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 10.7 years ago by ★ 1.3k • written 10.7 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
10.7 years ago Matthew McCall ▴ 830
0
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1
reply
1.5k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 10.7 years ago by 16k • written 10.7 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
10.8 years ago Brad Friedman ▴ 40
0
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1
reply
2.1k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ▴ 40
0
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2
replies
2.0k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 10.8 years ago by ▴ 20 • written 10.8 years ago by ★ 13k
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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 10.8 years ago by 68k • written 10.8 years ago by ▴ 600
0
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0
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1.4k
views
Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
10.8 years ago 张超 ▴ 50
0
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0
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1.7k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
10.8 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
10.9 years ago Kasper Daniel Hansen ★ 6.5k
0
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0
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1.7k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
10.9 years ago Brian Herb ▴ 80
0
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0
replies
2.3k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.9 years ago Elena Serrano ▴ 30
0
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1
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3.8k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ★ 13k
0
votes
0
replies
884
views
strange spam from biocbuild
PROcess PROcess
10.9 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.2k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.9 years ago by 68k • written 10.9 years ago by ★ 13k
0
votes
5
replies
1.7k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 11.0 years ago by 68k • written 11.0 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 11.0 years ago by 68k • written 11.0 years ago by ★ 13k
0
votes
0
replies
1.5k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
11.0 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
11.0 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
11.0 years ago Rory Stark ★ 5.2k
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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