filter=FALSE is not working in gdcDEAnalysis

rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC

Apache License 2.0

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filter=FALSE is not working in gdcDEAnalysis #1

Open fcgportal opened 6 years ago

fcgportal commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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~