User: Zach Brehm

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Zach Brehm0
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Posts by Zach Brehm

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Comment: C: Problem constructing DESeq objects with large integers.
... Yes, but to be safe I just double checked them with the following: ``` > max(assay(rse_merge)) - .Machine$integer.max [1] 13994598706 > any(is.na(assay(rse_merge))) [1] FALSE ``` ...
written 11 days ago by Zach Brehm0
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Problem constructing DESeq objects with large integers.
... Hello, I am attempting to construct a dds object out some GTEx data obtained through Recount. When creating the dds object, I am met with an error that I believe is due to integers in the data that are too large for R. I have been unable to find a workaround for this thus far. The following output ...
deseq2 recount written 11 days ago by Zach Brehm0
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Dexus: Responsibilities for samples in 3% of informative genes all fall into the main condition.
... I used the dexus function from the dexus package on a matrix of count data that had previously been normalized. After filtering the responsibilities matrix in the resulting object according to those genes labelled as "informative", roughly 3% of the remaining genes have exactly zero samples falling ...
dexus written 10 months ago by Zach Brehm0

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