having a weird problem. I wrote a package which me and my team use to analyse NGS data, in particular to extract and sanitize it from a complicated workflow. I then thought i would give DESeq2 a go, which i could not get to work for the life of me. For some reason I figured my package might be the reason, so i saved the sanitized data as an .Rdata file and tried to do the DESeq2 on the data without my own package loaded, which worked.
library(MyPackage) countsTable <- aBunchOfMyFunctions Group <- factor(SomeGroupNames) coldata1 <- data.frame(Group=Group, row.names = someRowNames ) dds <- DESeqDataSetFromMatrix(countData = countsTable, colData = coldata1, design = ~ Group ) dds <- DESeq(dds) using pre-existing size factors estimating dispersions found already estimated dispersions, replacing these gene-wise dispersion estimates Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame
If i save the data, restart, reload the data and start over without loading my package it works like a charm.
Whats going on? I'm guessing I might be overriding some function(s), but how do I tell which?