gravatar for susheelbhanu

4 hours ago by

Hi all,

I've used DESeq2 many times before, but for some reason, running into the below issue

Error in validObject(.Object) :    invalid class “DESeqDataSet”
object: superclass "RectangularData" not defined in the environment of
the object's class

My code is as follows:

BiocManager::install("DESeq2") 

library(DESeq2)

kegg_mg <- read.delim(here("kegg",

"aaron_metaG_KEGG_counts_merged.txt"), 
                      header=TRUE) %>% as.matrix()
y_mg <- data.frame(row.names=c("GM1a", "GM1b", "GM1c", "GM4a", "GM4b",
 "GM4c"), 
                 condition=as.factor(c(rep("GM1",3), rep("GM4",3))))

 ddsMat_mg <-DESeqDataSetFromMatrix(countData = kegg_mg, colData =
 y_mg, design = ~ condition)

I've restarted Rstudio. Purged all the existing packages and did a clean re-install, and still the problem persists. My input file is a table with 6 columns and count values.
Thank you for your help!



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