Showing : arrayexpress • reset
2
votes
2
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45
views
limma - removing samples?
ArrayExpress limma arrays
21 hours ago • updated 18 minutes ago RMP87 • 0
4
votes
2
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103
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TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 27 days ago by 56k • written 27 days ago by • 0
3
votes
2
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99
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
90
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 6 months ago by 56k • written 6 months ago by • 0
0
votes
2
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139
views
Regarding ArrayExpress package
microarray arrayexpress
updated 7 months ago by 56k • written 7 months ago by • 0
0
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0
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78
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ArrayExpress error when creating rawset
ArrayExpress arrayexpress
14 months ago Majeed MJ • 0
3
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4
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848
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 15 months ago by • 0 • written 2.3 years ago by • 0
2
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3
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517
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 2.3 years ago by 56k • written 2.3 years ago by • 0
3
votes
5
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1.0k
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 2.6 years ago by 42k • written 2.6 years ago by ▴ 780
1
vote
4
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642
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 10
1
vote
1
reply
336
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
0
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0
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349
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Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
3.2 years ago rfes • 0
0
votes
0
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291
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
3.2 years ago klv2706w ▴ 10
0
votes
2
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690
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 3.2 years ago by 56k • written 3.2 years ago by ▴ 230
0
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1
reply
533
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
3.5 years ago Andy91 ▴ 60
3
votes
6
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1.3k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 3.6 years ago by 13k • written 3.6 years ago by ▴ 590
4
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1
reply
749
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
3.9 years ago sandmann.t ▴ 70
0
votes
1
reply
715
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
4.3 years ago Andrew_McDavid ▴ 260
2
votes
1
reply
613
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 4.3 years ago by 56k • written 4.3 years ago by • 0
2
votes
3
replies
886
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 4.5 years ago by ▴ 20 • written 4.5 years ago by ▴ 130
0
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0
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527
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress microarray R
4.7 years ago deepue ▴ 10
0
votes
0
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589
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
4.8 years ago Steffen Neumann ▴ 30
0
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5
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762
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arrayExpress: problem running code from the vignette
arrayexpress
5.0 years ago kevin.rue ▴ 300
0
votes
1
reply
1.3k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 5.9 years ago by 56k • written 5.9 years ago by • 0
0
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3
replies
730
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Differential Expression of c.diff. microarray
arrayexpress differential expression
6.0 years ago SSK ▴ 10
0
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1
reply
734
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
6.0 years ago SSK ▴ 10
0
votes
1
reply
971
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 7.1 years ago by 56k • written 7.1 years ago by ★ 12k
0
votes
1
reply
918
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 7.2 years ago by 13k • written 7.2 years ago by ▴ 20
0
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5
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1.1k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 8.0 years ago by 21k • written 8.0 years ago by ▴ 720
2
votes
0
replies
678
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
8.2 years ago Ibrahim Emam ▴ 50
0
votes
0
replies
982
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
8.2 years ago Ibrahim Emam ▴ 50
0
votes
0
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875
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
8.2 years ago Mirza, Nasir ▴ 40
0
votes
2
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731
views
Error when using impute to get missing values
impute ArrayExpress impute ArrayExpress
updated 9.1 years ago by ★ 4.2k • written 9.1 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 9.2 years ago by 13k • written 9.2 years ago by ★ 12k
0
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2
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993
views
Odd warning in simpleaffy, using quality control
cdf probe simpleaffy ArrayExpress cdf probe simpleaffy ArrayExpress
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 720
0
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0
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756
views
Odd warning in simpleaffy, using quality control
cdf simpleaffy ArrayExpress cdf simpleaffy ArrayExpress
9.2 years ago David Westergaard ▴ 280
0
votes
1
reply
814
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 30
0
votes
1
reply
808
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 9.5 years ago by 6.4k • written 9.5 years ago by ★ 12k
0
votes
0
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614
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
9.6 years ago Stephen Turner ▴ 270
0
votes
0
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758
views
Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
9.6 years ago Claude Chelala ▴ 40
0
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5
replies
755
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 10.0 years ago by ★ 3.3k • written 10.0 years ago by ▴ 220
0
votes
1
reply
903
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 10.1 years ago by ★ 3.3k • written 10.1 years ago by ▴ 220
0
votes
14
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922
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 10.1 years ago by ★ 3.3k • written 10.1 years ago by ▴ 220
0
votes
1
reply
470
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 10.1 years ago by 13k • written 10.1 years ago by ▴ 10
0
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0
replies
594
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
10.1 years ago Gordon Smyth 42k
0
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0
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600
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
10.1 years ago Yong Li ▴ 190
0
votes
2
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1.4k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization convert ArrayExpress Normalization convert ArrayExpress
updated 10.2 years ago by ▴ 110 • written 10.2 years ago by ▴ 290
0
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0
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649
views
beadarray: how to create BeadStudio output after createBeadSummaryData
PROcess beadarray ArrayExpress PROcess beadarray ArrayExpress
10.3 years ago Cei Abreu-Goodger ▴ 830
0
votes
2
replies
792
views
Problem importing ArrayExpress data for custom array into BioConductor
Microarray cdf ArrayExpress Microarray cdf ArrayExpress
updated 10.5 years ago by 13k • written 10.6 years ago by ▴ 10
0
votes
3
replies
784
views
Error loading ArrayExpress in R 2.12 Mac
ArrayExpress ArrayExpress
updated 10.6 years ago by 21k • written 10.6 years ago by ▴ 550
97 results • Page 1 of 2
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Replies
Comment: How to download the ChAMP dependency ChAMPdata by shepherl 2.6k
You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…
Comment: DiffBind reporting error by Rory Stark ★ 3.8k
If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…
Comment: limma - removing samples? by RMP87 • 0
Thank you very much for the explanation. Making it more precise. Could I analyze and normalize all samples from a dataset even though I had…
Comment: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ? by Saulius • 0
Yes - I think you are right once more. Thanks for taking so much time to look into this. Size factors come in twice in the code of `cqn`: …
Comment: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ? by Michael Love 32k
Re: (2), I read the code and docs as adding in library size scaling, not removing. This is because, after (1) the offset is in the directi…
Votes
A: Using DADA2 output for DESeq2
Answer: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
Comment: Error wth Installation BiocManager
Answer: limma - removing samples?
Answer: limma - removing samples?
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