I load my idats into the environment and created the sigDF object. When I try to run openSesame to preprocess, I get an error. The code and the error message below:
#### Load idats ####
main_dir <- "." # main directory where idats are
idats <- searchIDATprefixes(dir.name = main_dir, recursive=TRUE, use.basename=TRUE) ## 1160
# Remove failed scans that were rescanned: Chip 207221060056
fail <- idats[grep("207221060056",idats)] # 8
idats <- idats[!idats%in%fail] # 1152
# Load
sdf <- lapply(idats, readIDATpair)
# Option 1: DB (similar to our minfi ssNoob)
MulticoreParam()
sdf_DB1 <- openSesame(sdf, prep="DB", func=NULL, BPPARAM = BiocParallel::MulticoreParam())
error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment
I tried the code with a single chip and it runs. So, I don't why I gives this error when I try to run in all samples. Can that be a memory issue? I have 1152 samples, but I didn't have a problem running a similar N with minfi.
I load my idats into the environment and created the sigDF object. When I try to run openSesame to preprocess, I get an error. The code and the error message below:
error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment
I tried the code with a single chip and it runs. So, I don't why I gives this error when I try to run in all samples. Can that be a memory issue? I have 1152 samples, but I didn't have a problem running a similar N with minfi.