Hi,
I am getting this error at the extract_modules step, which appears to be related to the maximum length of allowed vectors in R: https://stackoverflow.com/questions/42479854/merge-error-negative-length-vectors-are-not-allowed, alyssafrazee/polyester#41, https://support.bioconductor.org/p/66401/
"You are getting this error because the data.frame / data.table created by the join has more than 2^31 - 1 rows (2,147,483,647). Due to the way vectors are constructed internally by R, the maximum length of any vector is 2^31 - 1 elements (see: https://stackoverflow.com/a/5234293/2341679). Since a data.frame / data.table is really a list() of vectors, this limit also applies to the number of rows."
modules <- extract_modules(scale_quantile(expr_sel), traj$time, verbose = FALSE)
expr_sel is 48384 (cells) * 100 (top 100 genes from gene_importances)
Looking at my memory profiling output, there is a spike of memory usage at this point:
Is there a way around this, or would I need to subsample the number of cells? What is the maximum number of cells * genes for which you have run extract_modules. Looking at the underlying code, my guess is that the error arises when running Mclust.
Best wishes,
Lucy
Hi,
I am getting this error at the
extract_modulesstep, which appears to be related to the maximum length of allowed vectors in R: https://stackoverflow.com/questions/42479854/merge-error-negative-length-vectors-are-not-allowed, alyssafrazee/polyester#41, https://support.bioconductor.org/p/66401/expr_sel is 48384 (cells) * 100 (top 100 genes from
gene_importances)Looking at my memory profiling output, there is a spike of memory usage at this point:
Is there a way around this, or would I need to subsample the number of cells? What is the maximum number of cells * genes for which you have run
extract_modules. Looking at the underlying code, my guess is that the error arises when runningMclust.Best wishes,
Lucy