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 6 months ago by 67k • written 6 months ago by • 0
2
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2
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996
views
Simple queryAE command returning "Error: 1: Document is empty"
queryAE ArrayExpress
24 months 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 13 months ago by ▴ 40 • written 2.1 years ago by ▴ 20
2
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2
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1.2k
views
limma - removing samples?
ArrayExpress limma arrays
3.5 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 3.6 years ago by 67k • written 3.6 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 3.6 years ago by 51k • written 3.6 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 4.0 years ago by 67k • written 4.0 years ago by • 0
0
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2
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1.4k
views
Regarding ArrayExpress package
microarray arrayexpress
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
0
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0
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998
views
ArrayExpress error when creating rawset
ArrayExpress arrayexpress
4.7 years ago Majeed MJ • 0
3
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4
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3.4k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 4.7 years ago by • 0 • written 5.8 years ago by • 0
2
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3
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1.8k
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
6
votes
5
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3.5k
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 6.1 years ago by 51k • written 6.1 years ago by ▴ 830
1
vote
4
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2.3k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.6 years ago by 21k • written 6.6 years ago by ▴ 10
1
vote
1
reply
1.2k
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 6.6 years ago by 51k • written 6.6 years ago by • 0
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0
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1.1k
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.7 years ago rf • 0
0
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0
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958
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
6.7 years ago klv2706w ▴ 10
0
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2
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1.8k
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 6.7 years ago by 67k • written 6.7 years ago by ▴ 230
0
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1
reply
1.5k
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
7.0 years ago Andy91 ▴ 60
3
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6
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3.2k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 7.1 years ago by ★ 13k • written 7.1 years ago by ▴ 610
4
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1
reply
1.8k
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
7.4 years ago sandmann.t ▴ 70
0
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1
reply
1.5k
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
7.8 years ago Andrew_McDavid ▴ 270
2
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1
reply
1.4k
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 7.8 years ago by 67k • written 7.8 years ago by • 0
2
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3
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2.3k
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 8.0 years ago by ▴ 20 • written 8.0 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
8.2 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
8.3 years ago Steffen Neumann ▴ 30
0
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5
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2.1k
views
arrayExpress: problem running code from the vignette
arrayexpress
8.5 years ago kevin.rue ▴ 350
0
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1
reply
2.1k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 9.4 years ago by 67k • written 9.4 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
9.5 years ago SSK ▴ 10
0
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1
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1.4k
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
9.5 years ago SSK ▴ 10
0
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1
reply
1.8k
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 10.6 years ago by 67k • written 10.6 years ago by ★ 13k
0
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1
reply
1.6k
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 10.7 years ago by ★ 13k • written 10.7 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 11.5 years ago by 21k • written 11.5 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
11.6 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
11.7 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
11.7 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 12.6 years ago by ★ 4.2k • written 12.6 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 12.7 years ago by ★ 13k • written 12.7 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 12.7 years ago by ▴ 280 • written 12.7 years ago by ▴ 740
0
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0
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1.3k
views
Odd warning in simpleaffy, using quality control
cdf simpleaffy ArrayExpress cdf simpleaffy ArrayExpress
12.7 years ago David Westergaard ▴ 280
0
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1
reply
1.6k
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 13.0 years ago by ▴ 20 • written 13.0 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 13.0 years ago by 6.7k • written 13.0 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
13.1 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
13.1 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 13.5 years ago by ★ 3.6k • written 13.5 years ago by ▴ 220
0
votes
1
reply
1.7k
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 13.6 years ago by ★ 3.6k • written 13.6 years ago by ▴ 220
0
votes
14
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2.5k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 13.6 years ago by ★ 3.6k • written 13.6 years ago by ▴ 220
0
votes
1
reply
1.1k
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 10
0
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0
replies
1.1k
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
13.6 years ago Gordon Smyth 51k
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
13.6 years ago Yong Li ▴ 190
0
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2
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2.6k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization convert ArrayExpress Normalization convert ArrayExpress
updated 13.7 years ago by ▴ 110 • written 13.7 years ago by ▴ 340
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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: ESTMATE, MCPcounter, EPIC, xCell input by Kang • 0
These are not, as far as I know, bioconductor packages. You should query on the websites for those specific software programs. @[mapquest][…
Comment: Robust way of dealing with low number of samples for Differential Gene Expressio by Kang • 0
I believe that pseudo-bulking is a strong way to approach DE, as long as it is possible to reliably identify the cell type across data and …
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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