Showing : ArrayExpress • reset
6
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5
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3.8k
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How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
agilent microarrays limma arrayexpress NChannelSet
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 840
4
votes
5
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2.4k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 17 months ago by ▴ 40 • written 2.4 years ago by ▴ 20
4
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1
reply
1.9k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
7.8 years ago sandmann.t ▴ 70
4
votes
2
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1.6k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
3
votes
4
replies
3.8k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 5.1 years ago by • 0 • written 6.2 years ago by • 0
3
votes
2
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1.5k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 4.0 years ago by 52k • written 4.0 years ago by • 0
3
votes
6
replies
3.4k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 610
2
votes
1
reply
314
views
Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 4 months ago by 68k • written 4 months ago by • 0
2
votes
2
replies
1.3k
views
limma - removing samples?
ArrayExpress limma arrays
3.9 years ago RMP87 • 0
2
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2
replies
1.1k
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
2.4 years ago alekeuro ▴ 10
2
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3
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2.0k
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
votes
3
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2.6k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 8.3 years ago by ▴ 20 • written 8.4 years ago by ▴ 180
2
votes
1
reply
1.4k
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
2
votes
0
replies
1.4k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
12.0 years ago Ibrahim Emam ▴ 50
1
vote
4
replies
2.5k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 10
1
vote
1
reply
1.5k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
1
vote
1
reply
1.3k
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
0
votes
1
reply
1.1k
views
making ExpressionSet from ArrayExpress
convert ArrayExpress convert ArrayExpress
updated 18.2 years ago by ▴ 580 • written 18.2 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Software Engineer Position at the EBI, Cambridge UK
Microarray GUI ArrayExpress Microarray GUI ArrayExpress
18.6 years ago Misha Kapushesky ▴ 130
0
votes
0
replies
703
views
Re; MAGEML
ArrayExpress ArrayExpress
21.4 years ago Steffen Durinck ▴ 420
0
votes
0
replies
953
views
breast tissue cel files
hgu133a ArrayExpress hgu133a ArrayExpress
18.7 years ago Rafael A. Irizarry ★ 2.3k
0
votes
0
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875
views
CEL files of ALL data set
ArrayExpress ArrayExpress
16.5 years ago Talloen, Willem [PRDBE] ▴ 10
0
votes
1
reply
1.1k
views
Reg: Reading SMD data using ArrayExpress pacakage
ArrayExpress ArrayExpress
updated 14.8 years ago by ▴ 60 • written 14.8 years ago by ▴ 170
0
votes
1
reply
981
views
About ArrayExpress MAGE-TAB tools
Microarray ArrayExpress Microarray ArrayExpress
updated 16.5 years ago by 21k • written 16.5 years ago by ★ 2.0k
0
votes
4
replies
1.3k
views
Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]
Annotation Normalization Cancer limma ArrayExpress Annotation Normalization Cancer limma
updated 16.4 years ago by ▴ 30 • written 16.4 years ago by 52k
0
votes
0
replies
892
views
CEL files of ALL data set
ArrayExpress ArrayExpress
16.5 years ago Joern Toedling ▴ 730
0
votes
0
replies
1.2k
views
CAMDA08 Announcement. Deadline extension
Microarray ArrayExpress Microarray ArrayExpress
16.5 years ago Ana Conesa ▴ 340
0
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1
reply
1.2k
views
Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]
Annotation Normalization GO Cancer limma ArrayExpress Annotation Normalization GO Cancer
updated 16.4 years ago by ▴ 280 • written 16.4 years ago by 52k
0
votes
0
replies
1.2k
views
CAMDA conference program announcement / early booking discount until 12 Nov!
Microarray ArrayExpress Microarray ArrayExpress
16.4 years ago Dr. D. P. Kreil Boku ▴ 50
0
votes
1
reply
1.4k
views
ArrayExpress package error
ArrayExpress ArrayExpress
updated 16.4 years ago by ▴ 280 • written 16.4 years ago by ▴ 600
0
votes
1
reply
1.4k
views
CodeLink Package: Not a Codelink exported file.
codelink ArrayExpress codelink ArrayExpress
updated 19.0 years ago by ▴ 760 • written 19.0 years ago by ▴ 600
0
votes
0
replies
697
views
Re:MAGEML
ArrayExpress ArrayExpress
21.4 years ago Steffen Durinck ▴ 30
0
votes
0
replies
1.1k
views
RMAGEML installation and ArrayExpress database
RMAGEML ArrayExpress RMAGEML ArrayExpress
16.6 years ago John Lande ▴ 280
0
votes
2
replies
1.7k
views
Importing "Detailed sample annotation" from ArrayExpress DB into R
ArrayExpress ArrayExpress
16.6 years ago Markus Schmidberger ▴ 380
0
votes
0
replies
632
views
Fwd: Limma: How to read gene list, coordinates of sport when NO GAL file available
limma ArrayExpress limma ArrayExpress
19.0 years ago Gordon Smyth 52k
0
votes
1
reply
971
views
An importMAGEML problem in RMAGEML Package
RMAGEML ArrayExpress RMAGEML ArrayExpress
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
ArrayExpress error attaching phenodata
ArrayExpress ArrayExpress
updated 15.4 years ago by ▴ 280 • written 15.4 years ago by ★ 1.3k
0
votes
1
reply
1.3k
views
How to get platform annotation in ExpressionSet object
Annotation ArrayExpress Annotation ArrayExpress
updated 15.5 years ago by 21k • written 15.5 years ago by ▴ 30
0
votes
0
replies
1.5k
views
Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
13.5 years ago Claude Chelala ▴ 40
0
votes
0
replies
664
views
Limma: How to read gene list, coordinates of sport when NO GAL file available
limma ArrayExpress limma ArrayExpress
19.0 years ago Gordon Smyth 52k
0
votes
2
replies
1.1k
views
Annotating Illumina Data from ArrayExpress
convert ArrayExpress convert ArrayExpress
updated 15.4 years ago by ★ 7.2k • written 15.4 years ago by ▴ 260
0
votes
0
replies
850
views
Hapmap miRNA expression data
miRNA HapMap ArrayExpress miRNA HapMap ArrayExpress
15.3 years ago Paul Geeleher ★ 1.3k
0
votes
3
replies
1.4k
views
Reg: normalization of ArrayExpress data
Microarray Normalization GO ArrayExpress Microarray Normalization GO ArrayExpress
15.1 years ago Rohit Farmer ▴ 170
0
votes
1
reply
1.1k
views
Query regarding GEO Database
ArrayExpress ArrayExpress
updated 15.0 years ago by 21k • written 15.0 years ago by ▴ 120
0
votes
1
reply
966
views
Unable to get the Platform Table using fData on eset object
ArrayExpress ArrayExpress
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 30
0
votes
0
replies
1.0k
views
ArrayExpress User Survey
ArrayExpress ArrayExpress
14.9 years ago Wolfgang Huber ★ 13k
0
votes
3
replies
1.3k
views
mageml
ArrayExpress ArrayExpress
updated 21.4 years ago by 6.7k • written 21.4 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Reading SMD data in limma
limma ArrayExpress limma ArrayExpress
updated 14.8 years ago by ▴ 90 • written 14.8 years ago by ▴ 170
0
votes
2
replies
1.3k
views
Reading SMD data in limma
limma ArrayExpress limma ArrayExpress
14.8 years ago Gordon Smyth 52k
0
votes
2
replies
1.3k
views
rma error on an affyBatch from ArrayExpress?
ArrayExpress ArrayExpress
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 90
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Comment: Package developing and interoperation with Bioconductor by shepherl 4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference by Rohit • 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2? by Joshua Llano • 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
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Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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