Showing : ArrayExpress • reset
6
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5
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3.2k
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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 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
4
votes
2
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1.3k
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TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
4
votes
5
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1.9k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 7 months ago by ▴ 40 • written 18 months ago by ▴ 20
4
votes
1
reply
1.6k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
6.9 years ago sandmann.t ▴ 70
3
votes
6
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2.8k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 610
3
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4
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2.9k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 4.2 years ago by • 0 • written 5.3 years ago by • 0
3
votes
2
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1.2k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 3.1 years ago by 50k • written 3.1 years ago by • 0
2
votes
2
replies
803
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
17 months ago alekeuro ▴ 10
2
votes
1
reply
1.2k
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 7.3 years ago by 65k • written 7.3 years ago by • 0
2
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3
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2.0k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 7.4 years ago by ▴ 20 • written 7.5 years ago by ▴ 180
2
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3
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1.6k
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
2
votes
0
replies
1.2k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
11.1 years ago Ibrahim Emam ▴ 50
2
votes
2
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1.0k
views
limma - removing samples?
ArrayExpress limma arrays
3.0 years ago RMP87 • 0
1
vote
1
reply
1.1k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
1
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4
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2.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 6.1 years ago by 50k • written 6.1 years ago by • 0
0
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2
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1.0k
views
About ArrayExpress MAGE-TAB tools
Microarray GEOquery ArrayExpress Microarray GEOquery ArrayExpress
updated 15.9 years ago by ▴ 280 • written 15.9 years ago by ▴ 450
0
votes
0
replies
1.3k
views
Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
12.6 years ago Claude Chelala ▴ 40
0
votes
1
reply
831
views
An importMAGEML problem in RMAGEML Package
RMAGEML ArrayExpress RMAGEML ArrayExpress
updated 15.8 years ago by ★ 13k • written 15.8 years ago by ▴ 10
0
votes
2
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1.4k
views
Importing "Detailed sample annotation" from ArrayExpress DB into R
ArrayExpress ArrayExpress
15.7 years ago Markus Schmidberger ▴ 380
0
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0
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976
views
RMAGEML installation and ArrayExpress database
RMAGEML ArrayExpress RMAGEML ArrayExpress
15.7 years ago John Lande ▴ 280
0
votes
1
reply
838
views
About ArrayExpress MAGE-TAB tools
Microarray ArrayExpress Microarray ArrayExpress
updated 15.6 years ago by 21k • written 15.6 years ago by ★ 2.0k
0
votes
0
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761
views
CEL files of ALL data set
ArrayExpress ArrayExpress
15.6 years ago Talloen, Willem [PRDBE] ▴ 10
0
votes
4
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1.0k
views
Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]
Annotation Normalization Cancer limma ArrayExpress Annotation Normalization Cancer limma
updated 15.5 years ago by ▴ 30 • written 15.5 years ago by 50k
0
votes
0
replies
759
views
CEL files of ALL data set
ArrayExpress ArrayExpress
15.6 years ago Joern Toedling ▴ 730
0
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0
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1.0k
views
CAMDA08 Announcement. Deadline extension
Microarray ArrayExpress Microarray ArrayExpress
15.6 years ago Ana Conesa ▴ 340
0
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1
reply
1.0k
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 15.5 years ago by ▴ 280 • written 15.5 years ago by 50k
0
votes
0
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971
views
CAMDA conference program announcement / early booking discount until 12 Nov!
Microarray ArrayExpress Microarray ArrayExpress
15.5 years ago Dr. D. P. Kreil Boku ▴ 50
0
votes
1
reply
1.2k
views
ArrayExpress package error
ArrayExpress ArrayExpress
updated 15.5 years ago by ▴ 280 • written 15.5 years ago by ▴ 600
0
votes
5
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1.8k
views
Expressionset from ArrayExpress processed data
ArrayExpress SANTA ArrayExpress SANTA
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 20
0
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2
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1.3k
views
Limma - GenePix
ArrayExpress ArrayExpress
updated 14.9 years ago by ▴ 810 • written 14.9 years ago by ▴ 20
0
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5
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1.5k
views
Limma - GenePix
limma ArrayExpress limma ArrayExpress
updated 14.9 years ago by ▴ 810 • written 14.9 years ago by 50k
0
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0
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716
views
GenePix - Limma
ArrayExpress ArrayExpress
14.9 years ago Juana Arco ▴ 20
0
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0
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1.2k
views
How to use ExpressionSet for further Analysis
convert ArrayExpress convert ArrayExpress
14.8 years ago Md.Mamunur Rashid ▴ 260
0
votes
6
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1.8k
views
regarding package ArrayExpress
ArrayExpress ArrayExpress
updated 14.7 years ago by ▴ 280 • written 14.7 years ago by ▴ 70
0
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2
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2.2k
views
ArrayExpress as NChannelSet data into limma-compatible type
limma convert ArrayExpress SJava limma convert ArrayExpress SJava
updated 14.6 years ago by 25k • written 14.6 years ago by ▴ 60
0
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2
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1.1k
views
rma error on an affyBatch from ArrayExpress?
ArrayExpress ArrayExpress
updated 14.6 years ago by 25k • written 14.6 years ago by ▴ 90
0
votes
1
reply
1.1k
views
How to get platform annotation in ExpressionSet object
Annotation ArrayExpress Annotation ArrayExpress
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 30
0
votes
1
reply
1.1k
views
ArrayExpress error attaching phenodata
ArrayExpress ArrayExpress
updated 14.5 years ago by ▴ 280 • written 14.5 years ago by ★ 1.3k
0
votes
2
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970
views
Annotating Illumina Data from ArrayExpress
convert ArrayExpress convert ArrayExpress
updated 14.5 years ago by ★ 7.2k • written 14.5 years ago by ▴ 260
0
votes
0
replies
727
views
Hapmap miRNA expression data
miRNA HapMap ArrayExpress miRNA HapMap ArrayExpress
14.4 years ago Paul Geeleher ★ 1.3k
0
votes
3
replies
1.2k
views
Reg: normalization of ArrayExpress data
Microarray Normalization GO ArrayExpress Microarray Normalization GO ArrayExpress
14.2 years ago Rohit Farmer ▴ 170
0
votes
1
reply
959
views
Query regarding GEO Database
ArrayExpress ArrayExpress
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 120
0
votes
1
reply
814
views
Unable to get the Platform Table using fData on eset object
ArrayExpress ArrayExpress
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 30
0
votes
0
replies
818
views
ArrayExpress User Survey
ArrayExpress ArrayExpress
14.0 years ago Wolfgang Huber ★ 13k
0
votes
1
reply
952
views
Reg: Reading SMD data using ArrayExpress pacakage
ArrayExpress ArrayExpress
updated 13.9 years ago by ▴ 60 • written 13.9 years ago by ▴ 170
0
votes
1
reply
927
views
Reading SMD data in limma
limma ArrayExpress limma ArrayExpress
updated 13.9 years ago by ▴ 90 • written 13.9 years ago by ▴ 170
0
votes
2
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1.1k
views
Reading SMD data in limma
limma ArrayExpress limma ArrayExpress
13.9 years ago Gordon Smyth 50k
0
votes
2
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2.0k
views
ArrayExpress: missing cdf environment!
Cancer hgu133a cdf ArrayExpress Cancer hgu133a cdf ArrayExpress
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 110
0
votes
2
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1.3k
views
Problem importing ArrayExpress data for custom array into BioConductor
Microarray cdf ArrayExpress Microarray cdf ArrayExpress
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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