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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.9 years ago by 53k • written 17.0 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
4.2 years ago Shane • 0
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4
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21k
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XML package cannot be installed
PROcess PROcess
updated 7.9 years ago by • 0 • written 13.5 years ago by ★ 13k
0
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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 7.9 years ago by • 0 • written 12.0 years ago by ▴ 300
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deleted questions.. as its not very relevant..
process
8.6 years ago • updated 8.5 years ago bioDoctorate • 0
4
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8
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2.5k
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Designing a model matrix and further process?
limma annotation R process
8.5 years ago Biotechuos4 • 0
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8
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2.9k
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raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 8.9 years ago by ▴ 40 • written 19.4 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 9.2 years ago by • 0 • written 9.2 years ago by • 0
0
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1
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1.3k
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Error in reading file
process
updated 9.3 years ago by ★ 6.6k • written 9.3 years ago by • 0
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1.1k
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Use of the GeneMeta package
process
9.3 years ago m.batzenschlager • 0
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0
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1.4k
views
about keeping the processing results in the computer memory
process
9.4 years ago Bogdan ▴ 670
0
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7
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3.3k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 9.5 years ago by • 0 • written 15.8 years ago by ★ 1.6k
2
votes
9
replies
4.4k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 9.9 years ago by 6.7k • written 11.8 years ago by 68k
0
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0
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1.5k
views
Help for affy
affy process probe
10.0 years ago weizhong_2007 • 0
0
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1
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1.6k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 10.4 years ago by • 0 • written 21.0 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 10.5 years ago by • 0 • written 11.9 years ago by ★ 13k
0
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6
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2.7k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 10.8 years ago by • 0 • written 13.1 years ago by ▴ 40
0
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2
replies
2.2k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.9 years ago by • 0 • written 21.4 years ago by ▴ 600
0
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1
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2.1k
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 10.9 years ago by • 0 • written 14.6 years ago by ▴ 10
0
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1
reply
2.2k
views
MEDIPS quality control
process medips
updated 11.3 years ago by ▴ 570 • written 11.4 years ago by • 0
0
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1
reply
1.9k
views
champ package input
process
updated 11.3 years ago by 6.7k • written 11.3 years ago by • 0
1
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2
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6.5k
views
read .mat file in R
process
updated 11.4 years ago by ★ 3.0k • written 11.4 years ago by • 0
0
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1
reply
2.9k
views
Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 11.4 years ago by 1.6k • written 11.9 years ago by ★ 13k
0
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2
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5.4k
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getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 11.5 years ago by ▴ 80 • written 11.5 years ago by ▴ 30
0
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1
reply
2.0k
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Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 11.5 years ago by 21k • written 11.5 years ago by ▴ 20
0
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0
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2.7k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.5 years ago Bernd Fischer ▴ 550
0
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4
replies
2.8k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 11.5 years ago by 68k • written 11.6 years ago by ▴ 30
0
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2
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1.7k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 11.6 years ago by ★ 3.9k • written 11.6 years ago by ▴ 390
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 11.6 years ago by 21k • written 11.6 years ago by ▴ 190
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2.7k
views
DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 11.6 years ago by 43k • written 11.6 years ago by ▴ 20
1
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1
reply
2.7k
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How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ★ 13k
0
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0
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1.5k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
11.6 years ago Matthew McCall ▴ 830
0
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1
reply
1.6k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 90
0
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0
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1.5k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
11.6 years ago Brad Friedman ▴ 40
0
votes
1
reply
2.3k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 11.7 years ago by ★ 11k • written 11.7 years ago by ▴ 40
0
votes
2
replies
2.3k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 11.7 years ago by ▴ 20 • written 11.7 years ago by ★ 13k
0
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1
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1.6k
views
Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 11.7 years ago by 68k • written 11.7 years ago by ▴ 600
0
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0
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1.5k
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Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
11.7 years ago 张超 ▴ 50
0
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0
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1.9k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
11.7 years ago swarmqq@gmail.com ▴ 10
0
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0
replies
1.6k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
11.8 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
2.0k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
11.8 years ago Brian Herb ▴ 80
0
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0
replies
2.6k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
11.8 years ago Elena Serrano ▴ 30
0
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1
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4.1k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 13k
0
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0
replies
1.0k
views
strange spam from biocbuild
PROcess PROcess
11.8 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.3k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 11.8 years ago by 68k • written 11.8 years ago by ★ 13k
0
votes
5
replies
1.9k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 11.8 years ago by 68k • written 11.8 years ago by ▴ 110
0
votes
1
reply
2.4k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 11.9 years ago by 68k • written 11.9 years ago by ★ 13k
0
votes
0
replies
1.7k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
11.9 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
1.4k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
11.9 years ago James W. MacDonald 68k
0
votes
0
replies
1.9k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
11.9 years ago Rory Stark ★ 5.3k
651 results • Page 1 of 14
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Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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