Showing : expressionset • reset
8
votes
23
replies
4.7k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 12 months ago by ★ 3.4k • written 12 months ago by ▴ 50
6
votes
7
replies
4.4k
views
GOexpress: use DESeq2 data object as input
GOexpress deseq2 expressionset
9.5 years ago martin.hoelzer ▴ 20
5
votes
2
replies
1.2k
views
Is the ExpressionSet Class Deprecated?
expressionset
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 20
5
votes
7
replies
2.0k
views
Difficulty extending ExpressionSet
biobase expressionset eset
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 20
4
votes
3
replies
1.4k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
4
votes
8
replies
3.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma biobase ExpressionSet
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
3
votes
3
replies
2.1k
views
Error running CellMix SampleAnalysis vignette
software error cellmix vignette expressionset
8.3 years ago gabor.halasz • 0
3
votes
5
replies
1.9k
views
Get Gen-Expression values accross samples for ONE Gene given by Gene-Symbol
expressionset bioconductor
updated 8.6 years ago by ▴ 70 • written 8.6 years ago by • 0
3
votes
2
replies
2.9k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
3
votes
10
replies
2.9k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering bioconductor genesymbols expressionset
10.1 years ago svlachavas ▴ 840
3
votes
9
replies
2.0k
views
How many features an ExpressionSet can contain ?
ExpressionSet
2.9 years ago • updated 2.8 years ago OE • 0
2
votes
5
replies
5.5k
views
GSVA error - incomplete instalation?
GSVA ExpressionSet
9.4 years ago thrabe • 0
2
votes
1
reply
3.5k
views
ExpressionSet: Remove NA values above a certain threshold
expressionset
updated 9.7 years ago by ★ 28k • written 9.7 years ago by ▴ 30
2
votes
4
replies
2.2k
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 9.2 years ago by 25k • written 9.2 years ago by ▴ 840
1
vote
2
replies
576
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
13 months ago Mj.A. • 0
1
vote
2
replies
1.8k
views
How can I see that my samples is normalized or not?
Normalization ExpressionSet Series
updated 9.1 years ago by 68k • written 9.1 years ago by • 0
1
vote
1
reply
1.3k
views
Combining more than 2 ExpressionSets at the same time,
expressionset combine concatenate combineTwoExpressionSet
9.0 years ago g_draculla ▴ 10
1
vote
1
reply
1.3k
views
Generating ExpressionSet Objects
r expressionset subseq rnaseq
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 70
1
vote
3
replies
2.6k
views
Log-Transform Values of eSet
expressionset bioconductor limma geoquery
updated 8.5 years ago by ▴ 840 • written 8.5 years ago by • 0
1
vote
2
replies
3.5k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 8.5 years ago by 25k • written 8.5 years ago by ★ 4.1k
1
vote
10
replies
2.4k
views
Error when restore rownames of Feature data of ExpressionSet
expressionset
updated 7.6 years ago by 25k • written 7.6 years ago by • 0
0
votes
1
reply
1.5k
views
single probe represent multiple genes?
gcrma microarray expressionset
updated 8.2 years ago by ▴ 840 • written 8.2 years ago by ▴ 20
0
votes
3
replies
3.0k
views
Annotation in ExpressionSet object
ExpressionSet globaltest
8.9 years ago NS ▴ 60
0
votes
0
replies
1.2k
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
7.1 years ago rf • 0
0
votes
0
replies
1.1k
views
HTqPCR - unable to create a 'qPCRset' object
htqpcr expressionset
6.8 years ago jirkanov • 0
0
votes
0
replies
872
views
Computing se.exprs in R for an Expressionset?
microarray Expressionset se.exprs
6.7 years ago payam_delfani1980 • 0
0
votes
2
replies
1.3k
views
'GO_analyse' function error
goexpress ExpressionSet GO_analyse
5.6 years ago rezashiralmohammad • 0
0
votes
1
reply
1.6k
views
InSilicoMerging error when using merge
insilicomerging error insilicodb expressionset
8.2 years ago andreas.pittroff • 0
0
votes
1
reply
751
views
ExpressionSet: any shortcut for number-of-samples and number-of-features?
expressionSet
5.0 years ago aush ▴ 40
0
votes
6
replies
1.9k
views
expression correlation on an ExpressionSet
ExpressionSet caseControl Correlation Plot
updated 7.9 years ago by • 0 • written 8.2 years ago by ▴ 10
0
votes
1
reply
1.1k
views
beadarray error conversion
beadarray limma ExpressionSet
updated 8.4 years ago by 52k • written 8.4 years ago by • 0
0
votes
1
reply
938
views
Calculations (averaging and normalization) with expressionset
RTCA Biobase Bioconductor expressionset
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
votes
0
replies
1.6k
views
Export expressionSet to ArrayExpress "processed data"
expressionset simpleaffy arrayexpress tsv
8.7 years ago Steffen Neumann ▴ 30
0
votes
3
replies
3.0k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
ExpressionSet: Internal Standard
expressionset
updated 8.9 years ago by ★ 13k • written 8.9 years ago by • 0
0
votes
1
reply
1.4k
views
Problem Subsetting ExpressionSet
expressionset biobase bioconductor
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 60
36 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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