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filter=FALSE is not working in gdcDEAnalysis #1

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fcgportal opened this issue Jan 9, 2018 · 2 comments
Open

filter=FALSE is not working in gdcDEAnalysis #1

fcgportal opened this issue Jan 9, 2018 · 2 comments

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@fcgportal
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I am trying to keep all genes when did gdcDEAnalysis analysis.
My Arguments:
gdcDEAnalysis(counts, group, comparison, method = "limma", n.cores = NULL, filter = FALSE)
But it keep giving me filtered out results, no different from filter=TRUE.
Could you please help me out with it?
Thanks!

@fcgportal
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fcgportal commented Jan 9, 2018

P.S. DESeq2 in gdcDEAnalysis is not working as well.
My Arguments:
gdcDEAnalysis(counts, group, comparison, method = "DESeq2", n.cores = 4, filter = FALSE)
Error log:
Error in ncol(countData) == nrow(colData) : object 'readCounts' not found
No error reported when using limma or edgeR.

@Jialab-UCR
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Hi, I'm so sorry for the late response. We're working on all the problems collected from users. The final version could be available in a week. Thank you so much for the comments~

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