Showing : factor • reset
2
votes
2
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407
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How to extract factor levels of coldata from deseq object?
deseq2 levels factor colData
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
2
votes
3
replies
826
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GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges RaggedExperiment coercion logical factor
updated 3.8 years ago by 550 • written 3.8 years ago by • 0
3
votes
11
replies
2.0k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 4.1 years ago by ★ 2.6k • written 4.1 years ago by ▴ 30
0
votes
2
replies
834
views
GenomicRanges: `seqnames<-` can not work as expected
genomicranges seqnames factor
4.9 years ago wcstcyx ▴ 30
0
votes
0
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451
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Package in R to determine which factor values are overrepresented within a particular factor of interest
R overrrepresentation factor variable factor enrichment
4.9 years ago IOM ▴ 20
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Comment: Macbook M1 install genefilter failed by Alexandre • 0
Michael, Do you have perhaps R binary installed for Intel chips ?![enter image description here][1] [1]: /media/images/5d9b0f4e-18f6-…
Comment: Macbook M1 install genefilter failed by Alexandre • 0
[n] stops the installation. I've tried to force since it is installed already and then I tried `none` as you said. > BiocManager::inst…
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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