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7
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A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
0
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3
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4.8k
views
how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 22 months ago by • 0 • written 12.2 years ago by ★ 7.2k
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1
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1.6k
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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 2.1 years ago by 50k • written 15.2 years ago by ▴ 30
0
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0
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775
views
Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.4 years ago Shane • 0
0
votes
4
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19k
views
XML package cannot be installed
PROcess PROcess
updated 6.1 years ago by • 0 • written 11.8 years ago by ★ 13k
0
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8
replies
4.0k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 6.1 years ago by • 0 • written 10.2 years ago by ▴ 300
1
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2
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1.0k
views
deleted questions.. as its not very relevant..
process
6.8 years ago • updated 6.7 years ago bioDoctorate • 0
4
votes
8
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1.8k
views
Designing a model matrix and further process?
limma annotation R process
6.8 years ago Biotechuos4 • 0
0
votes
8
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1.9k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 7.1 years ago by ▴ 40 • written 17.6 years ago by ▴ 20
0
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8
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1.8k
views
`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
0
votes
1
reply
965
views
Error in reading file
process
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by • 0
0
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0
replies
840
views
Use of the GeneMeta package
process
7.5 years ago m.batzenschlager • 0
0
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0
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1.0k
views
about keeping the processing results in the computer memory
process
7.6 years ago Bogdan ▴ 670
0
votes
7
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2.2k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.7 years ago by • 0 • written 14.0 years ago by ★ 1.6k
2
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9
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3.4k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 8.1 years ago by 6.7k • written 10.0 years ago by 65k
0
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0
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1.2k
views
Help for affy
affy process probe
8.2 years ago weizhong_2007 • 0
0
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1
reply
1.2k
views
Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 8.6 years ago by • 0 • written 19.2 years ago by ▴ 320
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2
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1.7k
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 8.7 years ago by • 0 • written 10.1 years ago by ★ 13k
0
votes
6
replies
1.9k
views
is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 9.0 years ago by • 0 • written 11.3 years ago by ▴ 40
0
votes
2
replies
1.6k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 9.1 years ago by • 0 • written 19.6 years ago by ▴ 600
0
votes
1
reply
1.7k
views
Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 9.1 years ago by • 0 • written 12.8 years ago by ▴ 10
0
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1
reply
1.7k
views
MEDIPS quality control
process medips
updated 9.5 years ago by ▴ 570 • written 9.6 years ago by • 0
0
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1
reply
1.6k
views
champ package input
process
updated 9.5 years ago by 6.7k • written 9.5 years ago by • 0
1
vote
2
replies
5.8k
views
read .mat file in R
process
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
0
votes
1
reply
1.8k
views
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
0
votes
2
replies
3.8k
views
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
0
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1
reply
1.5k
views
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
0
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0
replies
2.3k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.7 years ago Bernd Fischer ▴ 550
0
votes
4
replies
2.2k
views
.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
0
votes
2
replies
1.2k
views
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
0
votes
6
replies
2.9k
views
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
0
votes
1
reply
2.3k
views
DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 9.8 years ago by 41k • written 9.8 years ago by ▴ 20
1
vote
1
reply
2.3k
views
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
votes
0
replies
1.2k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
9.8 years ago Matthew McCall ▴ 830
0
votes
1
reply
1.3k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 90
0
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0
replies
1.2k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.8 years ago Brad Friedman ▴ 40
0
votes
1
reply
1.9k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 40
0
votes
2
replies
1.8k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ★ 13k
0
votes
1
reply
1.2k
views
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
0
votes
0
replies
1.2k
views
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
0
votes
0
replies
1.5k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
9.9 years ago swarmqq@gmail.com ▴ 10
0
votes
0
replies
1.3k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.0 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.5k
views
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
0
votes
0
replies
2.1k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
0
votes
1
reply
3.3k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ★ 13k
0
votes
0
replies
738
views
strange spam from biocbuild
PROcess PROcess
10.0 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.0k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.0 years ago by 65k • written 10.0 years ago by ★ 13k
0
votes
5
replies
1.5k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 10.1 years ago by 65k • written 10.0 years ago by ▴ 110
0
votes
1
reply
1.9k
views
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
0
votes
0
replies
1.3k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
10.1 years ago Kipper Fletez-Brant ▴ 150
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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