User: ErickF

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ErickF • 20
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Posts by ErickF

<prev • 6 results • page 1 of 1 • next >
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Answer: A: DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative
... Figured it out! The problem: I had replaced the original rownames in ex3 (the SE object) from entrezID numbers (which make zero sense to me) to gene symbols (which at least make some sense). I didn't think changing the rownames would matter so long as they matched rowdata, but it seems that was the ...
written 3.1 years ago by ErickF • 20
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Comment: C: DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative
... Hi Tom -- thanks. I tried rowRanges=rowdata but got the same error. Then I thought maybe if I defined rowdata by using rowdata <- rowData(ex3) (instead of rowRanges); and then I just omitted rowdata altogether, and still the same problem... The only difference I can find between my data is that ...
written 3.1 years ago by ErickF • 20
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DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
... Hi, I'm trying to run DEseq2. As a test I'm using RNAseq data from 8 samples.  My countdata, coldata, and rowdata objects look (to me) formatted as they should, the dimensions/lengths match, count data is correct, etc. But when I run DESeqDataSetFromMatrix() I get this error: > ddsFull <- DE ...
rnaseq deseq2 deseqdataset deseqdatasetfrommatrix written 3.1 years ago by ErickF • 20
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Comment: C: Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
... Will definitely try those --thanks! ...
written 3.1 years ago by ErickF • 20
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Answer: A: Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
... Update: Seems like indeed this was related to computing power (memory, cores, or something). I tried with smaller files and it worked. So I added a yieldSize parameter to BamFileList when creating "bamLst", to limit the number of reads scanned from the file at one time: bamLst <- BamFileList(fi ...
written 3.1 years ago by ErickF • 20
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Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
... Hi, I recently started working with RNAseq data. I used the code below to try to read 2-4 BAM files (BAM and BAI in the same directory, etc) but I repeatedly get the following error when running summarizeOverlaps(): Error: stop worker failed:   'clear_cluster' receive data failed:   reached elapse ...
rnaseq summarizeoverlaps bplapply read counting rangedsummarizedexperiment written 3.1 years ago by ErickF • 20

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
Scholar 3.1 years ago, created an answer that has been accepted. For A: Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
Scholar 3.1 years ago, created an answer that has been accepted. For A: DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative
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