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Showing :
arrayexpress
•
reset
2
votes
2
replies
763
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE
ArrayExpress
16 months ago
alekeuro
▴ 10
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 5 months ago by
jacorvar
▴ 40 • written 17 months ago by
eraldagjika
▴ 20
1
vote
2
replies
965
views
limma - removing samples?
ArrayExpress
limma
arrays
2.9 years ago
RMP87
• 0
4
votes
2
replies
1.3k
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Gero
• 0
3
votes
2
replies
1.1k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Gero
• 0
0
votes
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 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
Julie
• 0
0
votes
2
replies
1.1k
views
Regarding ArrayExpress package
microarray
arrayexpress
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
akanksha17arora
• 0
0
votes
0
replies
774
views
ArrayExpress error when creating rawset
ArrayExpress
arrayexpress
4.1 years ago
Majeed MJ
• 0
3
votes
4
replies
2.9k
views
lm.fit incompatible dimensions
oligo
arrayexpress
limma
updated 4.1 years ago by
Anna Woods
• 0 • written 5.2 years ago by
maxininfa
• 0
2
votes
3
replies
1.6k
views
Could not access the Bioconductor repository
bioconductor
proxy
arrayexpress
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
maxininfa
• 0
6
votes
5
replies
3.1k
views
How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
agilent microarrays
limma
arrayexpress
NChannelSet
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
svlachavas
▴ 830
1
vote
4
replies
1.9k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 6.0 years ago by
Sean Davis
21k • written 6.0 years ago by
arbet003
▴ 10
1
vote
1
reply
1.0k
views
Agilent Data Normalization Result
limma
agilent
arrayexpress
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
trandiemnghi
• 0
0
votes
0
replies
941
views
Error in building expression set for ArrayExpress
microarray
expressionset
arrayexpress
bioconductor
r
6.0 years ago
rf
• 0
0
votes
0
replies
800
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
6.1 years ago
klv2706w
▴ 10
0
votes
2
replies
1.6k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
Ed Siefker
▴ 230
0
votes
1
reply
1.3k
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress
twochannel
microarray
6.4 years ago
Andy91
▴ 60
3
votes
6
replies
2.8k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress
xml
rcurl
http
EBI
updated 6.5 years ago by
Wolfgang Huber
★ 13k • written 6.5 years ago by
Bernd Klaus
▴ 610
4
votes
1
reply
1.6k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress
ArrayExpress
hthgu133a.db
6.8 years ago
sandmann.t
▴ 70
0
votes
1
reply
1.3k
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
7.1 years ago
Andrew_McDavid
▴ 270
2
votes
1
reply
1.2k
views
Output of ArrayExpress() function
oligo
oligoclasses
arrayexpress
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
ste0891
• 0
2
votes
3
replies
2.0k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 7.3 years ago by
ugis
▴ 20 • written 7.4 years ago by
Keith Hughitt
▴ 180
0
votes
0
replies
1.0k
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress
microarray
R
7.6 years ago
deepue
▴ 10
0
votes
0
replies
1.3k
views
Export expressionSet to ArrayExpress "processed data"
expressionset
simpleaffy
arrayexpress
tsv
7.7 years ago
Steffen Neumann
▴ 30
0
votes
5
replies
1.8k
views
arrayExpress: problem running code from the vignette
arrayexpress
7.9 years ago
kevin.rue
▴ 350
0
votes
1
reply
1.9k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
Srinivasa R. Rao
• 0
0
votes
3
replies
1.3k
views
Differential Expression of c.diff. microarray
arrayexpress
differential expression
8.9 years ago
SSK
▴ 10
0
votes
1
reply
1.3k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress
differential expression
8.9 years ago
SSK
▴ 10
0
votes
1
reply
1.6k
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 10.0 years ago by
James W. MacDonald
65k • written 10.0 years ago by
Guest User
★ 13k
0
votes
1
reply
1.5k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics
ArrayExpress
arrayQualityMetrics
ArrayExpress
updated 10.1 years ago by
Wolfgang Huber
★ 13k • written 10.1 years ago by
Laurent.Pays
▴ 20
0
votes
5
replies
1.8k
views
XML package - 500 internal server error
GEOquery
ArrayExpress
GEOquery
ArrayExpress
updated 10.9 years ago by
Sean Davis
21k • written 10.9 years ago by
boczniak767
▴ 720
2
votes
0
replies
1.2k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress
ArrayExpress
11.0 years ago
Ibrahim Emam
▴ 50
0
votes
0
replies
1.7k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress
ArrayExpress
11.1 years ago
Ibrahim Emam
▴ 50
0
votes
0
replies
1.3k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress
ArrayExpress
11.1 years ago
Mirza, Nasir
▴ 40
0
votes
2
replies
1.3k
views
Error when using impute to get missing values
impute
ArrayExpress
impute
ArrayExpress
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
David Westergaard
▴ 10
0
votes
1
reply
2.0k
views
Error by using gpr data with marray
limma
marray
ArrayExpress
limma
marray
ArrayExpress
updated 12.1 years ago by
Wolfgang Huber
★ 13k • written 12.1 years ago by
Guest User
★ 13k
0
votes
2
replies
1.8k
views
Odd warning in simpleaffy, using quality control
cdf
probe
simpleaffy
ArrayExpress
cdf
probe
simpleaffy
ArrayExpress
updated 12.1 years ago by
David Westergaard
▴ 280 • written 12.1 years ago by
boczniak767
▴ 720
0
votes
0
replies
1.2k
views
Odd warning in simpleaffy, using quality control
cdf
simpleaffy
ArrayExpress
cdf
simpleaffy
ArrayExpress
12.1 years ago
David Westergaard
▴ 280
0
votes
1
reply
1.4k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress
ArrayExpress
updated 12.3 years ago by
audrey kauffmann
▴ 20 • written 12.3 years ago by
Mikhail Spivakov
▴ 30
0
votes
1
reply
1.4k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress
ArrayExpress
updated 12.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
12.4 years ago
Stephen Turner
▴ 290
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
12.5 years ago
Claude Chelala
▴ 40
0
votes
5
replies
1.5k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization
probe
limma
safe
ArrayExpress
Normalization
probe
limma
safe
ArrayExpress
updated 12.9 years ago by
Wei Shi
★ 3.6k • written 12.9 years ago by
Gavin Koh
▴ 220
0
votes
1
reply
1.5k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization
probe
safe
ArrayExpress
Normalization
probe
safe
ArrayExpress
updated 13.0 years ago by
Wei Shi
★ 3.6k • written 13.0 years ago by
Gavin Koh
▴ 220
0
votes
14
replies
2.2k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe
limma
ArrayExpress
probe
limma
ArrayExpress
updated 13.0 years ago by
Wei Shi
★ 3.6k • written 13.0 years ago by
Gavin Koh
▴ 220
0
votes
1
reply
957
views
magetab2bioc error
ArrayExpress
ArrayExpress
updated 13.0 years ago by
Wolfgang Huber
★ 13k • written 13.0 years ago by
pratibha mani
▴ 10
0
votes
0
replies
996
views
limma design problem with a two color dataset
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
13.0 years ago
Gordon Smyth
50k
0
votes
0
replies
1.0k
views
limma design problem with a two color dataset
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
13.0 years ago
Yong Li
▴ 190
0
votes
2
replies
2.3k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization
convert
ArrayExpress
Normalization
convert
ArrayExpress
updated 13.1 years ago by
Sole Acha, Xavi
▴ 110 • written 13.1 years ago by
Andreas Heider
▴ 340
0
votes
0
replies
1.1k
views
beadarray: how to create BeadStudio output after createBeadSummaryData
PROcess
beadarray
ArrayExpress
PROcess
beadarray
ArrayExpress
13.2 years ago
Cei Abreu-Goodger
▴ 830
50 results • Page
1 of 1
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Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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