Showing : ArrayExpress • reset
0
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 6 days ago by 65k • written 7 days ago by • 0
4
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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
2
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2
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805
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
17 months ago alekeuro ▴ 10
2
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2
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1.0k
views
limma - removing samples?
ArrayExpress limma arrays
3.0 years ago RMP87 • 0
4
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2
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1.3k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
3
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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
1
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1
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1.2k
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
0
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2
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1.2k
views
Regarding ArrayExpress package
microarray arrayexpress
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
0
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0
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818
views
ArrayExpress error when creating rawset
ArrayExpress arrayexpress
4.2 years ago Majeed MJ • 0
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
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
6
votes
5
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3.2k
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 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
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
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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
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0
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979
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Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.1 years ago rf • 0
0
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0
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827
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
6.2 years ago klv2706w ▴ 10
0
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2
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1.6k
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 230
0
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1
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1.3k
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
6.5 years ago Andy91 ▴ 60
3
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6
replies
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
4
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1
reply
1.6k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
6.9 years ago sandmann.t ▴ 70
0
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1
reply
1.3k
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
7.2 years ago Andrew_McDavid ▴ 270
2
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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 7.5 years ago by ▴ 20 • written 7.5 years ago by ▴ 180
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0
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1.0k
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress microarray R
7.7 years ago deepue ▴ 10
0
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0
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1.3k
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
7.8 years ago Steffen Neumann ▴ 30
0
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5
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1.8k
views
arrayExpress: problem running code from the vignette
arrayexpress
8.0 years ago kevin.rue ▴ 350
0
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1
reply
2.0k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
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3
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1.4k
views
Differential Expression of c.diff. microarray
arrayexpress differential expression
9.0 years ago SSK ▴ 10
0
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1
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1.3k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
9.0 years ago SSK ▴ 10
0
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1
reply
1.7k
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 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
0
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1
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1.5k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 20
0
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5
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1.9k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 11.0 years ago by 21k • written 11.0 years ago by ▴ 720
2
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0
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1.2k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
11.1 years ago Ibrahim Emam ▴ 50
0
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0
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1.7k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
11.2 years ago Ibrahim Emam ▴ 50
0
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0
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1.3k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
11.2 years ago Mirza, Nasir ▴ 40
0
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2
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1.4k
views
Error when using impute to get missing values
impute ArrayExpress impute ArrayExpress
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 10
0
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1
reply
2.1k
views
Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ★ 13k
0
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2
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1.8k
views
Odd warning in simpleaffy, using quality control
cdf probe simpleaffy ArrayExpress cdf probe simpleaffy ArrayExpress
updated 12.2 years ago by ▴ 280 • written 12.2 years ago by ▴ 720
0
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0
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1.2k
views
Odd warning in simpleaffy, using quality control
cdf simpleaffy ArrayExpress cdf simpleaffy ArrayExpress
12.2 years ago David Westergaard ▴ 280
0
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1
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1.5k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 12.4 years ago by ▴ 20 • written 12.4 years ago by ▴ 30
0
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1
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1.4k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 12.4 years ago by 6.7k • written 12.5 years ago by ★ 13k
0
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0
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1.1k
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
12.6 years ago Stephen Turner ▴ 290
0
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0
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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
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5
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1.6k
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Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 13.0 years ago by ★ 3.6k • written 13.0 years ago by ▴ 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 13.1 years ago by ★ 3.6k • written 13.1 years ago by ▴ 220
0
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14
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2.3k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 13.1 years ago by ★ 3.6k • written 13.1 years ago by ▴ 220
0
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1
reply
981
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 13.1 years ago by ★ 13k • written 13.1 years ago by ▴ 10
0
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0
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1.0k
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.1 years ago Gordon Smyth 50k
0
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0
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1.0k
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.1 years ago Yong Li ▴ 190
0
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2
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2.4k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization convert ArrayExpress Normalization convert ArrayExpress
updated 13.2 years ago by ▴ 110 • written 13.2 years ago by ▴ 340
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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