User: l.s.wijaya

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l.s.wijaya0
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Posts by l.s.wijaya

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... Since the development branch of DESeq2 will be in 1 month, I will try to use the parallelization. I will keep an eye on the update. Thanks a lot for the helps!! ...
written 5 days ago by l.s.wijaya0
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... By the way, is there any way I can use a function to spread the cores for results(). For instance, like deseq(), I can use BIOPARAM to spread the worker. This would be super helpful if I can do this stuff for results(). I tried to use mclapply for instance, bus still the results() was only performed ...
written 5 days ago by l.s.wijaya0
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... Currently, I am trying to subset the outcome matrix of DESeq(). However, I encountered errors written above, What do you mean running results() on pairs? Perhaps, if I manage to subset the matrix, I can run nbinomWaldTest() and calculate the log 2 FC with results(). ...
written 6 days ago by l.s.wijaya0
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... That would be great to try the second option. Thanks a lot. However, is there anything worth trying to solve this issue? I mean, like any way to subset the dds large matrix. I can also consider to use the first option. ...
written 6 days ago by l.s.wijaya0
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... in total I have 845 samples, each sample has 21111 genes. The samples per group vary depending on the group. Some, I have 6 only, but some I have 116. In total, I have 8 groups so that I plan to subset the matrix into 8 parts. ...
written 6 days ago by l.s.wijaya0
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Subset-ing Large DESeqDataSet for data extraction with contrast function
... Hi all, I am now running Deseq2 analysis. However, I am stuck at extracting the results with results(dds, contrast = ()) after deseq() from the large DESeqDataSet. The problem was, it took me extremely long to only extract one comparison (3 hours/comparison meanwhile, I have 265 comparison to extra ...
deseq2 written 6 days ago by l.s.wijaya0 • updated 6 days ago by Michael Love25k

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