User: ErickF
ErickF • 20
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Posts by ErickF
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... 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 3.4 years ago by
ErickF • 20
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... 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 3.4 years ago by
ErickF • 20
1
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3.2k
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... 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 ...
written 3.4 years ago by
ErickF • 20
0
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... Will definitely try those --thanks!
...
written 3.4 years ago by
ErickF • 20
2
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1
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2.0k
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... 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 3.4 years ago by
ErickF • 20
4
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2.0k
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... 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 ...
written 3.4 years ago by
ErickF • 20
Latest awards to ErickF
Popular Question
3.4 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
3.4 years ago,
created a question with more than 1,000 views.
For Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
Scholar
3.4 years ago,
created an answer that has been accepted.
For A: Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
Scholar
3.4 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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