User: b.cox

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Posts by b.cox

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Answer: A: DESEQ2 VST sample number limits?
... variancestabilizingtransformation() crashed and produced no object returne4d. I am trying with vst(). if I can find the time I will try some different sizes and setting to determine what the cost is to increase the sample and gene dimensions, as it could be good to know. ...
written 2.9 years ago by b.cox0
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Answer: A: DESEQ2 VST sample number limits?
... Thinking of Michael's answer above. The example in the DESeq2 manual stated that 20 samples by 1000 genes took on the order of 5 seconds. this is 20K data features or about 4K/sec. My smaller data set of 12 million features took about 4 hours to process, but if vst were linear it would take 0.8 hour ...
written 2.9 years ago by b.cox0
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Comment: C: DESEQ2 VST sample number limits?
... Thanks for the reply. I saw the new vst() function now. It increases speed through sub-sampling. I was concerned about this for the performance as it is already an estimate and it was not clear if the sampling routine would also need to be optimized for the data set. A 1000 genes might be representa ...
written 2.9 years ago by b.cox0
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DESEQ2 VST sample number limits?
... Hi, I have been using variancestabilizingtransformation for normalizing single cell RNA-seq data. I have assembled a large data set of >1500 cells (samples) that contain information on about 40,000 genes. variancestabilizingtransformation has been running for about 24 hours. Will this process fi ...
deseq2 size variancestabilizingtransformation limits written 2.9 years ago by b.cox0

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Scholar 2.9 years ago, created an answer that has been accepted. For A: DESEQ2 VST sample number limits?

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