Showing : ArrayExpress • reset
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Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 14.0 years ago by ★ 3.6k • written 14.0 years ago by ▴ 220
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8
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3.7k
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Reading Agilent files using read.maimages
Survival DynDoc genefilter tkWidgets affy vsn marray convert ArrayExpress Survival affy
updated 17.6 years ago by ▴ 20 • written 17.6 years ago by ▴ 100
3
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6
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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
0
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6
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2.1k
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regarding package ArrayExpress
ArrayExpress ArrayExpress
updated 15.6 years ago by ▴ 280 • written 15.6 years ago by ▴ 70
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5
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2.3k
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arrayExpress: problem running code from the vignette
arrayexpress
8.9 years ago kevin.rue ▴ 350
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
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5
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2.1k
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Expressionset from ArrayExpress processed data
ArrayExpress SANTA ArrayExpress SANTA
updated 16.2 years ago by 25k • written 16.2 years ago by ▴ 20
0
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5
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2.2k
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XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 11.9 years ago by 21k • written 11.9 years ago by ▴ 740
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5
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1.7k
views
Limma - GenePix
limma ArrayExpress limma ArrayExpress
updated 15.8 years ago by ▴ 810 • written 15.8 years ago by 52k
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
0
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5
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3.6k
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loading processed data into eset class
ArrayExpress ArrayExpress
updated 14.7 years ago by 6.7k • written 14.7 years ago by ▴ 90
0
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5
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1.9k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 13.9 years ago by ★ 3.6k • written 13.9 years ago by ▴ 220
0
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4
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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
1
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4
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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
3
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4
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3.8k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 5.1 years ago by • 0 • written 6.2 years ago by • 0
0
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3
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1.4k
views
Reg: normalization of ArrayExpress data
Microarray Normalization GO ArrayExpress Microarray Normalization GO ArrayExpress
15.1 years ago Rohit Farmer ▴ 170
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
0
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3
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1.6k
views
Differential Expression of c.diff. microarray
arrayexpress differential expression
9.9 years ago SSK ▴ 10
0
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3
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661
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
0
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3
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views
mageml
ArrayExpress ArrayExpress
updated 21.4 years ago by 6.7k • written 21.4 years ago by ▴ 20
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3
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1.7k
views
Error loading ArrayExpress in R 2.12 Mac
ArrayExpress ArrayExpress
updated 14.4 years ago by 21k • written 14.4 years ago by ▴ 550
2
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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
0
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2
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1.6k
views
Error when using impute to get missing values
impute ArrayExpress impute ArrayExpress
updated 13.0 years ago by ★ 4.2k • written 13.0 years ago by ▴ 10
4
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2
replies
1.6k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
votes
2
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1.1k
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
2.4 years ago alekeuro ▴ 10
0
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2
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1.3k
views
Reading SMD data in limma
limma ArrayExpress limma ArrayExpress
14.8 years ago Gordon Smyth 52k
0
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2
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1.5k
views
Regarding ArrayExpress package
microarray arrayexpress
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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2
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1.7k
views
Importing "Detailed sample annotation" from ArrayExpress DB into R
ArrayExpress ArrayExpress
16.6 years ago Markus Schmidberger ▴ 380
2
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2
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1.3k
views
limma - removing samples?
ArrayExpress limma arrays
3.9 years ago RMP87 • 0
0
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2
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2.8k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization convert ArrayExpress Normalization convert ArrayExpress
updated 14.1 years ago by ▴ 110 • written 14.1 years ago by ▴ 340
0
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2
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1.1k
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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
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2
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1.9k
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 230
0
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2
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1.2k
views
About ArrayExpress MAGE-TAB tools
Microarray GEOquery ArrayExpress Microarray GEOquery ArrayExpress
updated 16.8 years ago by ▴ 280 • written 16.8 years ago by ▴ 450
0
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2
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1.5k
views
Problem importing ArrayExpress data for custom array into BioConductor
Microarray cdf ArrayExpress Microarray cdf ArrayExpress
updated 14.4 years ago by ★ 13k • written 14.4 years ago by ▴ 10
0
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2
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2.1k
views
Odd warning in simpleaffy, using quality control
cdf probe simpleaffy ArrayExpress cdf probe simpleaffy ArrayExpress
updated 13.1 years ago by ▴ 280 • written 13.1 years ago by ▴ 740
0
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2
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1.6k
views
Limma - GenePix
ArrayExpress ArrayExpress
updated 15.8 years ago by ▴ 810 • written 15.8 years ago by ▴ 20
0
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2
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2.5k
views
ArrayExpress as NChannelSet data into limma-compatible type
limma convert ArrayExpress SJava limma convert ArrayExpress SJava
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 60
0
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2
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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
0
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2
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2.2k
views
ArrayExpress: missing cdf environment!
Cancer hgu133a cdf ArrayExpress Cancer hgu133a cdf ArrayExpress
updated 14.5 years ago by ★ 13k • written 14.5 years ago by ▴ 110
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
0
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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
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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
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1
reply
1.9k
views
Reading MAGE-ML cdf into bioconductor for limma in R v. 3.0.2
Microarray cdf probe makecdfenv RMAGEML ArrayExpress Microarray cdf probe makecdfenv
updated 11.0 years ago by 68k • written 11.0 years ago by ★ 13k
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
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1
reply
876
views
RMAGEML installation and ArrayExpress database
Cancer RMAGEML ArrayExpress Cancer RMAGEML ArrayExpress
16.6 years ago Martin Morgan 25k
0
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1
reply
1.7k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 20
0
votes
1
reply
1.6k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
9.9 years ago SSK ▴ 10
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
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
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
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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!
Votes
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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