Showing : expressionSet • reset
8
votes
23
replies
848
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 13 days ago by ★ 3.3k • written 15 days ago by ▴ 40
1
vote
10
replies
1.8k
views
Error when restore rownames of Feature data of ExpressionSet
expressionset
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
3
votes
10
replies
2.3k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering bioconductor genesymbols expressionset
9.1 years ago svlachavas ▴ 830
3
votes
9
replies
1.4k
views
How many features an ExpressionSet can contain ?
ExpressionSet
22 months ago OE • 0
4
votes
8
replies
2.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma biobase ExpressionSet
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
5
votes
7
replies
1.5k
views
Difficulty extending ExpressionSet
biobase expressionset eset
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 20
6
votes
7
replies
3.7k
views
GOexpress: use DESeq2 data object as input
GOexpress deseq2 expressionset
8.5 years ago martin.hoelzer ▴ 20
0
votes
6
replies
1.5k
views
expression correlation on an ExpressionSet
ExpressionSet caseControl Correlation Plot
updated 6.9 years ago by • 0 • written 7.2 years ago by ▴ 10
2
votes
5
replies
3.9k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
8.4 years ago thrabe • 0
3
votes
5
replies
1.6k
views
Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
expressionset bioconductor
updated 7.6 years ago by ▴ 70 • written 7.6 years ago by • 0
2
votes
4
replies
1.9k
views
Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
expressionset limma annotation affymetrix microarrays
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 830
0
votes
3
replies
2.5k
views
Annotation in ExpressionSet object
ExpressionSet globaltest
7.9 years ago NS ▴ 60
4
votes
3
replies
1.2k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
3
votes
3
replies
1.8k
views
Error running CellMix SampleAnalysis vignette
software error cellmix vignette expressionset
7.3 years ago gabor.halasz • 0
0
votes
3
replies
2.1k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 21 months ago by 65k • written 21 months ago by • 0
1
vote
3
replies
2.2k
views
Log-Transform Values of eSet
expressionset bioconductor limma geoquery
updated 7.5 years ago by ▴ 830 • written 7.5 years ago by • 0
1
vote
2
replies
218
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
4 weeks ago • updated 29 days ago Mj.A. • 0
1
vote
2
replies
1.4k
views
How can I see that my samples is normalized or not?
Normalization ExpressionSet Series
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
1
vote
2
replies
3.0k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 3.9k
0
votes
2
replies
985
views
'GO_analyse' function error
goexpress ExpressionSet GO_analyse
4.6 years ago rezashiralmohammad • 0
3
votes
2
replies
2.3k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
5
votes
2
replies
844
views
Is the ExpressionSet Class Deprecated?
expressionset
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 20
0
votes
1
reply
921
views
beadarray error conversion
beadarray limma ExpressionSet
updated 7.4 years ago by 50k • written 7.4 years ago by • 0
1
vote
1
reply
1.1k
views
Generating ExpressionSet Objects
r expressionset subseq rnaseq
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 70
0
votes
1
reply
1.2k
views
single probe represent multiple genes?
gcrma microarray expressionset
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Problem Subsetting ExpressionSet
expressionset biobase bioconductor
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 60
0
votes
1
reply
1.4k
views
InSilicoMerging error when using merge
insilicomerging error insilicodb expressionset
7.2 years ago andreas.pittroff • 0
0
votes
1
reply
963
views
ExpressionSet: Internal Standard
expressionset
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
1
vote
1
reply
1.0k
views
Combining more than 2 ExpressionSets at the same time,
expressionset combine concatenate combineTwoExpressionSet
8.0 years ago g_draculla ▴ 10
0
votes
1
reply
501
views
ExpressionSet: any shortcut for number-of-samples and number-of-features?
expressionSet
4.0 years ago aush ▴ 40
2
votes
1
reply
3.1k
views
ExpressionSet: Remove NA values above a certain threshold
expressionset
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 30
0
votes
1
reply
680
views
Calculations (averaging and normalization) with expressionset
RTCA Biobase Bioconductor expressionset
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
0
votes
0
replies
967
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
6.1 years ago rf • 0
0
votes
0
replies
852
views
HTqPCR - unable to create a 'qPCRset' object
htqpcr expressionset
5.8 years ago jirkanov • 0
0
votes
0
replies
723
views
Computing se.exprs in R for an Expressionset?
microarray Expressionset se.exprs
5.7 years ago payam_delfani1980 • 0
0
votes
0
replies
1.3k
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
7.7 years ago Steffen Neumann ▴ 30
36 results • Page 1 of 1
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Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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