Showing : ArrayExpress • reset
2
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203
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
0
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3
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561
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
2
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2
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1.0k
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
2.1 years ago alekeuro ▴ 10
4
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5
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2.3k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 15 months ago by ▴ 40 • written 2.2 years ago by ▴ 20
2
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2
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1.3k
views
limma - removing samples?
ArrayExpress limma arrays
3.6 years ago RMP87 • 0
4
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2
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1.5k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.7 years ago by 67k • written 3.7 years ago by • 0
3
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2
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1.4k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
1
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1
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1.4k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
0
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2
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1.4k
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Regarding ArrayExpress package
microarray arrayexpress
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
0
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0
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1.0k
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ArrayExpress error when creating rawset
ArrayExpress arrayexpress
4.9 years ago Majeed MJ • 0
3
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4
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3.6k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 4.9 years ago by • 0 • written 6.0 years ago by • 0
2
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3
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1.9k
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
6
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5
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3.6k
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 6.3 years ago by 52k • written 6.3 years ago by ▴ 840
1
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4
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2.4k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.7 years ago by 21k • written 6.7 years ago by ▴ 10
1
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1
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1.3k
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
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0
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1.2k
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Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.8 years ago rf • 0
0
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0
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982
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
6.8 years ago klv2706w ▴ 10
0
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2
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1.8k
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 6.8 years ago by 67k • written 6.8 years ago by ▴ 230
0
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1
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1.6k
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
7.2 years ago Andy91 ▴ 60
3
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6
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3.3k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ▴ 610
4
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1
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1.8k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
7.5 years ago sandmann.t ▴ 70
0
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1
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1.6k
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
7.9 years ago Andrew_McDavid ▴ 270
2
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1
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1.4k
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 7.9 years ago by 67k • written 7.9 years ago by • 0
2
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3
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2.4k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by ▴ 180
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0
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1.2k
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress microarray R
8.4 years ago deepue ▴ 10
0
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0
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1.5k
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
8.4 years ago Steffen Neumann ▴ 30
0
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5
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2.2k
views
arrayExpress: problem running code from the vignette
arrayexpress
8.7 years ago kevin.rue ▴ 350
0
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1
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2.1k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
0
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3
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1.5k
views
Differential Expression of c.diff. microarray
arrayexpress differential expression
9.7 years ago • updated 9.6 years ago SSK ▴ 10
0
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1
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1.5k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
9.7 years ago SSK ▴ 10
0
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1
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1.9k
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 10.8 years ago by 67k • written 10.8 years ago by ★ 13k
0
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1
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1.7k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 20
0
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5
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2.1k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 11.7 years ago by 21k • written 11.7 years ago by ▴ 740
2
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0
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1.3k
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
11.8 years ago Ibrahim Emam ▴ 50
0
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0
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1.8k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
11.8 years ago Ibrahim Emam ▴ 50
0
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0
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1.4k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
11.9 years ago Mirza, Nasir ▴ 40
0
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2
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1.6k
views
Error when using impute to get missing values
impute ArrayExpress impute ArrayExpress
updated 12.8 years ago by ★ 4.2k • written 12.8 years ago by ▴ 10
0
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1
reply
2.2k
views
Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ★ 13k
0
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2
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2.0k
views
Odd warning in simpleaffy, using quality control
cdf probe simpleaffy ArrayExpress cdf probe simpleaffy ArrayExpress
updated 12.8 years ago by ▴ 280 • written 12.8 years ago by ▴ 740
0
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0
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1.4k
views
Odd warning in simpleaffy, using quality control
cdf simpleaffy ArrayExpress cdf simpleaffy ArrayExpress
12.8 years ago David Westergaard ▴ 280
0
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1
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1.7k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 13.1 years ago by ▴ 20 • written 13.1 years ago by ▴ 30
0
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1
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1.6k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 13.1 years ago by 6.7k • written 13.1 years ago by ★ 13k
0
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0
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1.3k
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.2 years ago Stephen Turner ▴ 290
0
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0
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1.4k
views
Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
13.2 years ago Claude Chelala ▴ 40
0
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5
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1.8k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 13.7 years ago by ★ 3.6k • written 13.7 years ago by ▴ 220
0
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1
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1.8k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 13.7 years ago by ★ 3.6k • written 13.7 years ago by ▴ 220
0
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14
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2.6k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 13.7 years ago by ★ 3.6k • written 13.7 years ago by ▴ 220
0
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1
reply
1.1k
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 10
0
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0
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1.1k
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.8 years ago Gordon Smyth 52k
0
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0
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1.2k
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.8 years ago Yong Li ▴ 190
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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