Showing : arrayexpress • reset
1
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2
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164
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limma - removing samples?
ArrayExpress limma arrays
11 weeks ago • updated 10 weeks ago RMP87 • 0
4
votes
2
replies
168
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TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3 months ago by 57k • written 3 months ago by • 0
3
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2
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169
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NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
reply
121
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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 9 months ago by 57k • written 9 months ago by • 0
0
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2
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228
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Regarding ArrayExpress package
microarray arrayexpress
updated 10 months ago by 57k • written 10 months ago by • 0
0
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0
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107
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ArrayExpress error when creating rawset
ArrayExpress arrayexpress
17 months ago Majeed MJ • 0
3
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4
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929
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 17 months ago by • 0 • written 2.5 years ago by • 0
2
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3
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563
views
Could not access the Bioconductor repository
bioconductor proxy arrayexpress
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
3
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5
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1.1k
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 2.9 years ago by 43k • written 2.9 years ago by ▴ 780
1
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4
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736
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 10
1
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1
reply
370
views
Agilent Data Normalization Result
limma agilent arrayexpress
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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0
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380
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
3.4 years ago rfes • 0
0
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0
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321
views
Why procset(files, procol) requires exactly one column name?
ArrayExpress
3.4 years ago klv2706w ▴ 10
0
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2
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736
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 3.4 years ago by 57k • written 3.4 years ago by ▴ 230
0
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1
reply
570
views
Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
3.8 years ago Andy91 ▴ 60
3
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6
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1.4k
views
function getAE from ArrayExpress needs update because EBI has switched to https
arrayexpress xml rcurl http EBI
updated 3.8 years ago by 13k • written 3.8 years ago by ▴ 600
4
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1
reply
822
views
Mismatched ArrayExpress microarray annotation package
arrayexpress ArrayExpress hthgu133a.db
4.1 years ago sandmann.t ▴ 70
0
votes
1
reply
745
views
ArrayExpress fails with experiments without array data but could still return parsed .idf and .sdrf
ArrayExpress
4.5 years ago Andrew_McDavid ▴ 260
2
votes
1
reply
647
views
Output of ArrayExpress() function
oligo oligoclasses arrayexpress
updated 4.5 years ago by 57k • written 4.5 years ago by • 0
2
votes
3
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978
views
ArrayExpress unable to find raw data: "Experiment has no raw files available"
arrayexpress
updated 4.7 years ago by ▴ 20 • written 4.7 years ago by ▴ 140
0
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0
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552
views
error while using queryAE function for human transcription profiling experiments
ArrayExpress microarray R
4.9 years ago deepue ▴ 10
0
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0
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620
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Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
5.0 years ago Steffen Neumann ▴ 30
0
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5
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833
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arrayExpress: problem running code from the vignette
arrayexpress
5.2 years ago kevin.rue ▴ 300
0
votes
1
reply
1.3k
views
Error while reading ArrayExpress dataset
arrayexpress
updated 6.1 years ago by 57k • written 6.1 years ago by • 0
0
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3
replies
770
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Differential Expression of c.diff. microarray
arrayexpress differential expression
6.2 years ago SSK ▴ 10
0
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1
reply
790
views
ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
6.2 years ago SSK ▴ 10
0
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1
reply
1.0k
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 7.3 years ago by 57k • written 7.3 years ago by ★ 12k
0
votes
1
reply
949
views
Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
arrayQualityMetrics ArrayExpress arrayQualityMetrics ArrayExpress
updated 7.4 years ago by 13k • written 7.4 years ago by ▴ 20
0
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5
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1.1k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 8.2 years ago by 21k • written 8.2 years ago by ▴ 720
2
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0
replies
714
views
Fix for queryAE() in the ArrayExpress package
ArrayExpress ArrayExpress
8.4 years ago Ibrahim Emam ▴ 50
0
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0
replies
1.0k
views
Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
8.4 years ago Ibrahim Emam ▴ 50
0
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0
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916
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Loading eSet.r objects from ArrayExpress
ArrayExpress ArrayExpress
8.5 years ago Mirza, Nasir ▴ 40
0
votes
2
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764
views
Error when using impute to get missing values
impute ArrayExpress impute ArrayExpress
updated 9.3 years ago by ★ 4.2k • written 9.3 years ago by ▴ 10
0
votes
1
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1.3k
views
Error by using gpr data with marray
limma marray ArrayExpress limma marray ArrayExpress
updated 9.4 years ago by 13k • written 9.4 years ago by ★ 12k
0
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2
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1.1k
views
Odd warning in simpleaffy, using quality control
cdf probe simpleaffy ArrayExpress cdf probe simpleaffy ArrayExpress
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by ▴ 720
0
votes
0
replies
787
views
Odd warning in simpleaffy, using quality control
cdf simpleaffy ArrayExpress cdf simpleaffy ArrayExpress
9.4 years ago David Westergaard ▴ 280
0
votes
1
reply
844
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 9.7 years ago by ▴ 20 • written 9.7 years ago by ▴ 30
0
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1
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848
views
ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
ArrayExpress ArrayExpress
updated 9.7 years ago by 6.5k • written 9.7 years ago by ★ 12k
0
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0
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641
views
Problem with limma for two-color factorial design - Coefficients not estimable
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
9.8 years ago Stephen Turner ▴ 270
0
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0
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790
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Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
9.8 years ago Claude Chelala ▴ 40
0
votes
5
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805
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 10.2 years ago by ★ 3.3k • written 10.2 years ago by ▴ 220
0
votes
1
reply
937
views
Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 10.3 years ago by ★ 3.3k • written 10.3 years ago by ▴ 220
0
votes
14
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989
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 10.3 years ago by ★ 3.3k • written 10.3 years ago by ▴ 220
0
votes
1
reply
497
views
magetab2bioc error
ArrayExpress ArrayExpress
updated 10.3 years ago by 13k • written 10.3 years ago by ▴ 10
0
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0
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619
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
10.3 years ago Gordon Smyth 43k
0
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0
replies
624
views
limma design problem with a two color dataset
Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress
10.4 years ago Yong Li ▴ 190
0
votes
2
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1.4k
views
comparing HG-U219 data to HG-U133 data from public databases
Normalization convert ArrayExpress Normalization convert ArrayExpress
updated 10.4 years ago by ▴ 110 • written 10.4 years ago by ▴ 290
0
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0
replies
679
views
beadarray: how to create BeadStudio output after createBeadSummaryData
PROcess beadarray ArrayExpress PROcess beadarray ArrayExpress
10.5 years ago Cei Abreu-Goodger ▴ 830
0
votes
2
replies
823
views
Problem importing ArrayExpress data for custom array into BioConductor
Microarray cdf ArrayExpress Microarray cdf ArrayExpress
updated 10.8 years ago by 13k • written 10.8 years ago by ▴ 10
0
votes
3
replies
813
views
Error loading ArrayExpress in R 2.12 Mac
ArrayExpress ArrayExpress
updated 10.8 years ago by 21k • written 10.8 years ago by ▴ 550
50 results • Page 1 of 1
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Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx for the advice about the reference levels, in which I did do as you suggested! In fact, I even tried more options just want to see why…
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels by Gordon Smyth 43k
> is there a way to incorporate also the information of the additional samples that lack any of the aforementioned levels? NA values are n…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by James W. MacDonald 57k
The `voomLmFit` function will automatically fit a linear mixed model accounting for within-subject correlations if you block on patient, so…
Comment: error in getBM (biomaRt): "error: no such table: metadata" by Mike Smith ★ 5.0k
Thanks for providing this solution. Anyone else encountering the issue can test if the cache is a problem by running `getBM()` with the ar…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by svlachavas ▴ 780
Dear James, thank you very much for your comment; please excuse me for my naïve additional question, but is there an example in the edgeR …
Votes
tximeta error in fetching genome info
Answer: error in getBM (biomaRt): "error: no such table: metadata"
C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: cannot install edgeR on M1 Mac
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