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Showing :
arrayexpress
•
reset
2
votes
2
replies
218
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE
ArrayExpress
11 weeks ago
alekeuro
• 0
3
votes
3
replies
539
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 3 months ago by
James W. MacDonald
62k • written 3 months ago by
eraldagjika
▴ 20
1
vote
2
replies
523
views
limma - removing samples?
ArrayExpress
limma
arrays
21 months ago
RMP87
• 0
4
votes
2
replies
741
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 22 months ago by
James W. MacDonald
62k • written 22 months ago by
Gero
• 0
3
votes
2
replies
648
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 22 months ago by
Gordon Smyth
47k • written 22 months ago by
Gero
• 0
0
votes
1
reply
444
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress
methylationArrayAnalysis
updated 2.3 years ago by
James W. MacDonald
62k • written 2.3 years ago by
Julie
• 0
0
votes
2
replies
718
views
Regarding ArrayExpress package
microarray
arrayexpress
updated 2.4 years ago by
James W. MacDonald
62k • written 2.4 years ago by
akanksha17arora
• 0
0
votes
0
replies
389
views
ArrayExpress error when creating rawset
ArrayExpress
arrayexpress
3.0 years ago
Majeed MJ
• 0
3
votes
4
replies
1.9k
views
lm.fit incompatible dimensions
oligo
arrayexpress
limma
updated 3.0 years ago by
Anna Woods
• 0 • written 4.1 years ago by
maxininfa
• 0
2
votes
3
replies
977
views
Could not access the Bioconductor repository
bioconductor
proxy
arrayexpress
updated 4.1 years ago by
James W. MacDonald
62k • written 4.1 years ago by
maxininfa
• 0
6
votes
5
replies
2.2k
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 4.4 years ago by
Gordon Smyth
47k • written 4.4 years ago by
svlachavas
▴ 800
1
vote
4
replies
1.3k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 4.8 years ago by
Sean Davis
21k • written 4.8 years ago by
arbet003
▴ 10
1
vote
1
reply
704
views
Agilent Data Normalization Result
limma
agilent
arrayexpress
updated 4.9 years ago by
Gordon Smyth
47k • written 4.9 years ago by
trandiemnghi
• 0
0
votes
0
replies
640
views
Error in building expression set for ArrayExpress
microarray
expressionset
arrayexpress
bioconductor
r
4.9 years ago
rf
• 0
0
votes
0
replies
508
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
4.9 years ago
klv2706w
▴ 10
0
votes
2
replies
1.1k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 4.9 years ago by
James W. MacDonald
62k • written 4.9 years ago by
Ed Siefker
▴ 230
0
votes
1
reply
840
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress
twochannel
microarray
5.3 years ago
Andy91
▴ 60
3
votes
6
replies
2.0k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress
xml
rcurl
http
EBI
updated 5.3 years ago by
Wolfgang Huber
13k • written 5.4 years ago by
Bernd Klaus
▴ 600
4
votes
1
reply
1.2k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress
ArrayExpress
hthgu133a.db
5.6 years ago
sandmann.t
▴ 70
0
votes
1
reply
991
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
6.0 years ago
Andrew_McDavid
▴ 260
2
votes
1
reply
886
views
Output of ArrayExpress() function
oligo
oligoclasses
arrayexpress
updated 6.0 years ago by
James W. MacDonald
62k • written 6.0 years ago by
ste0891
• 0
2
votes
3
replies
1.5k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 6.2 years ago by
ugis
▴ 20 • written 6.2 years ago by
Keith Hughitt
▴ 180
0
votes
0
replies
774
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress
microarray
R
6.5 years ago
deepue
▴ 10
0
votes
0
replies
903
views
Export expressionSet to ArrayExpress "processed data"
expressionset
simpleaffy
arrayexpress
tsv
6.5 years ago
Steffen Neumann
▴ 30
0
votes
5
replies
1.2k
views
arrayExpress: problem running code from the vignette
arrayexpress
6.8 years ago
kevin.rue
▴ 320
0
votes
1
reply
1.6k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 7.6 years ago by
James W. MacDonald
62k • written 7.6 years ago by
Srinivasa R. Rao
• 0
0
votes
3
replies
1.0k
views
Differential Expression of c.diff. microarray
arrayexpress
differential expression
7.8 years ago
SSK
▴ 10
0
votes
1
reply
1.1k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress
differential expression
7.8 years ago
SSK
▴ 10
0
votes
1
reply
1.3k
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 8.9 years ago by
James W. MacDonald
62k • written 8.9 years ago by
Guest User
★ 12k
0
votes
1
reply
1.2k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics
ArrayExpress
arrayQualityMetrics
ArrayExpress
updated 8.9 years ago by
Wolfgang Huber
13k • written 9.0 years ago by
Laurent.Pays
▴ 20
0
votes
5
replies
1.4k
views
XML package - 500 internal server error
GEOquery
ArrayExpress
GEOquery
ArrayExpress
updated 9.8 years ago by
Sean Davis
21k • written 9.8 years ago by
Maciej Jończyk
▴ 720
2
votes
0
replies
911
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress
ArrayExpress
9.9 years ago
Ibrahim Emam
▴ 50
0
votes
0
replies
1.4k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress
ArrayExpress
9.9 years ago
Ibrahim Emam
▴ 50
0
votes
0
replies
1.1k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress
ArrayExpress
10.0 years ago
Mirza, Nasir
▴ 40
0
votes
2
replies
972
views
Error when using impute to get missing values
impute
ArrayExpress
impute
ArrayExpress
updated 10.9 years ago by
Tim Triche
★ 4.2k • written 10.9 years ago by
David Westergaard
▴ 10
0
votes
1
reply
1.7k
views
Error by using gpr data with marray
limma
marray
ArrayExpress
limma
marray
ArrayExpress
updated 10.9 years ago by
Wolfgang Huber
13k • written 10.9 years ago by
Guest User
★ 12k
0
votes
2
replies
1.4k
views
Odd warning in simpleaffy, using quality control
cdf
probe
simpleaffy
ArrayExpress
cdf
probe
simpleaffy
ArrayExpress
updated 10.9 years ago by
David Westergaard
▴ 280 • written 11.0 years ago by
Maciej Jończyk
▴ 720
0
votes
0
replies
962
views
Odd warning in simpleaffy, using quality control
cdf
simpleaffy
ArrayExpress
cdf
simpleaffy
ArrayExpress
11.0 years ago
David Westergaard
▴ 280
0
votes
1
reply
1.1k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress
ArrayExpress
updated 11.2 years ago by
audrey kauffmann
▴ 20 • written 11.2 years ago by
Mikhail Spivakov
▴ 30
0
votes
1
reply
1.1k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress
ArrayExpress
updated 11.2 years ago by
Vincent J. Carey, Jr.
6.6k • written 11.2 years ago by
Guest User
★ 12k
0
votes
0
replies
808
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
11.3 years ago
Stephen Turner
▴ 290
0
votes
0
replies
989
views
Bioinformatics course - October 2011 Registration is now open
Microarray
Cancer
biomaRt
ArrayExpress
genomes
SANTA
Microarray
Cancer
biomaRt
genomes
11.3 years ago
Claude Chelala
▴ 40
0
votes
5
replies
1.0k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization
probe
limma
safe
ArrayExpress
Normalization
probe
limma
safe
ArrayExpress
updated 11.8 years ago by
Wei Shi
★ 3.5k • written 11.8 years ago by
Gavin Koh
▴ 220
0
votes
1
reply
1.2k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization
probe
safe
ArrayExpress
Normalization
probe
safe
ArrayExpress
updated 11.8 years ago by
Wei Shi
★ 3.5k • written 11.8 years ago by
Gavin Koh
▴ 220
0
votes
14
replies
1.4k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe
limma
ArrayExpress
probe
limma
ArrayExpress
updated 11.8 years ago by
Wei Shi
★ 3.5k • written 11.8 years ago by
Gavin Koh
▴ 220
0
votes
1
reply
662
views
magetab2bioc error
ArrayExpress
ArrayExpress
updated 11.9 years ago by
Wolfgang Huber
13k • written 11.9 years ago by
pratibha mani
▴ 10
0
votes
0
replies
772
views
limma design problem with a two color dataset
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
11.9 years ago
Gordon Smyth
47k
0
votes
0
replies
768
views
limma design problem with a two color dataset
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
11.9 years ago
Yong Li
▴ 190
0
votes
2
replies
1.8k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization
convert
ArrayExpress
Normalization
convert
ArrayExpress
updated 11.9 years ago by
Sole Acha, Xavi
▴ 110 • written 11.9 years ago by
Andreas Heider
▴ 340
0
votes
0
replies
835
views
beadarray: how to create BeadStudio output after createBeadSummaryData
PROcess
beadarray
ArrayExpress
PROcess
beadarray
ArrayExpress
12.1 years ago
Cei Abreu-Goodger
▴ 830
50 results • Page
1 of 1
Recent ...
Replies
Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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