Showing : ArrayExpress • reset
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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 41 minutes ago by 65k • written 1 day ago by • 0
2
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2
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797
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Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
17 months ago alekeuro ▴ 10
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 6 months ago by ▴ 40 • written 18 months ago by ▴ 20
2
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2
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1.0k
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limma - removing samples?
ArrayExpress limma arrays
3.0 years ago RMP87 • 0
4
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2
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1.3k
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TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.0 years ago by 65k • written 3.0 years ago by • 0
3
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2
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1.2k
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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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1.1k
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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
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2
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1.2k
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Regarding ArrayExpress package
microarray arrayexpress
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
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0
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812
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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
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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
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Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
6
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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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972
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Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.1 years ago rf • 0
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0
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823
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
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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
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2.8k
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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
6.8 years ago sandmann.t ▴ 70
0
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1
reply
1.3k
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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
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1.2k
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 7.2 years ago by 65k • written 7.2 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 7.4 years ago by ▴ 20 • written 7.4 years ago by ▴ 180
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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
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0
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1.3k
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
7.7 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
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1.9k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
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3
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1.4k
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Differential Expression of c.diff. microarray
arrayexpress differential expression
9.0 years ago SSK ▴ 10
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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
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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 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
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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
11.1 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
2.0k
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 12.4 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
12.5 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
views
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 13.0 years ago by ★ 3.6k • written 13.0 years ago by ▴ 220
0
votes
14
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2.2k
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
votes
1
reply
978
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: Help with error using camera() in limma by Chris • 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
Answer: Help with error using camera() in limma by James W. MacDonald 65k
The first step should be to read the help page, which says ``` Usage: ## Default S3 method: camera(y, index, design, cont…
Comment: Assist me in determining whether the analysis process using the limma package ha by James W. MacDonald 65k
The description of the analysis says there are 120 genes at a 1.5 fold change and a p<0.05. They don't mention any multiplicity correction.…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
When using `arrayWeights()`, you mean the variability within the same group, is that correct? I alway run `arrayWeights()` because I naive …
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Sey R. • 0
Thank you for your response
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Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
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