cibersortx error - $ operator is invalid for atomic vectors

good day good people,

after a day chasing after double quotes and other non printable characters in my file, I checked for duplicated annotation as well and nothing. I give up and I humbly ask for help. I want to use cibersortx to deconvolute the cell composition of a sample of Plasmodium falciparum. The signature matrix was successfully generated as well as the GEP. I still get that error:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': $ operator is invalid for atomic vectors
Calls: CIBERSORTxGEP ... CIBERSORTxFractions -> CoreAlg -> t -> .handleSimpleError -> h
In addition: Warning message:
In mclapply(1:svn_itor, res, mc.cores = svn_itor) :
  all scheduled cores encountered errors in user code
Execution halted

here is a screenshot of my mixture table

Can somebody please help me thank you in advance, Franck

cibersortx

• 964 views • link

written 1.4 years ago by Franck •

1 answer

I finally found the reason of the mistake. The initial scRNA seq dataset I used to generate the the signature matrix came from a paper and I didn't pay attention that the geneID had dots and underscores. It was a conflict between my geneID formats.

• 0 views • link

written 1.3 years ago by Franck •