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 19 days ago by 65k • written 20 days ago by • 0
2
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2
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818
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Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
18 months ago alekeuro ▴ 10
4
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5
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2.0k
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time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 7 months ago by ▴ 40 • written 19 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 3.1 years ago by 65k • written 3.1 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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1.2k
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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 3.6 years ago by 65k • written 3.6 years ago by • 0
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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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831
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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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3.0k
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lm.fit incompatible dimensions
oligo arrayexpress limma
updated 4.3 years ago by • 0 • written 5.4 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 5.4 years ago by 65k • written 5.4 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 5.7 years ago by 50k • written 5.7 years ago by ▴ 830
1
vote
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 6.2 years ago by 50k • written 6.2 years ago by • 0
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Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.2 years ago rf • 0
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0
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841
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
6.6 years ago Andy91 ▴ 60
3
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6
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2.9k
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
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1
reply
1.4k
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
7.3 years ago Andrew_McDavid ▴ 270
2
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1
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1.3k
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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1.0k
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress microarray R
7.8 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
7.8 years ago Steffen Neumann ▴ 30
0
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5
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1.9k
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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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
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1
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1.3k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
9.1 years ago SSK ▴ 10
0
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1
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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
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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
11.2 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
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0
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1.3k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
11.3 years ago Mirza, Nasir ▴ 40
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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 12.2 years ago by ★ 4.2k • written 12.2 years ago by ▴ 10
0
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1
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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
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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
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1.2k
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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 12.5 years ago by ▴ 20 • written 12.5 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 12.5 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
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1.3k
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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 13.1 years ago by ★ 3.6k • written 13.1 years ago by ▴ 220
0
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1
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1.6k
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
votes
1
reply
990
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 13.2 years ago by ★ 13k • written 13.2 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
13.2 years ago Gordon Smyth 50k
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
13.2 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: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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