This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in deconvolution using CIBERSORTx

I am currently using CIBERSORTx for the deconvolution of cell types. I made a mixture file of samples (TPM counts) using R that looks like this - enter image description here

But whenever I try to use this mixture file against any signature matrix it give me this error -

Error in file(file, "rt") : cannot open the connection
Calls: CIBERSORTxFractions -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'files/soumya.yadavxxxxxx@xxxx.xxx.in/NP': No such file or directory
Execution halted.

Can anyone help me resolve this? Thankyou.

cibersortx deconvolution
• 1,042 views • link
updated by Aspire Aspire • written by yadavsoumya647 • yadavsoumya647

1 answer

When something similar happened to me, re-uploading the file worked. Also double-check that the name of the file is written in a way that is suitable for computers (no spaces, and it should probably have the ".txt" extension)

• 0 views • link
written by Aspire Aspire

Hi! Thanks for replying. I tried doing all of that multiple times but its still not working.

• 0 views • link
written by yadavsoumya647 • yadavsoumya647

hi, i checked and formatted the file name again and uploaded it and it worked! Thankyou for your help!!

• 0 views • link
written by yadavsoumya647 • yadavsoumya647

Log in to answer this question.

More posts like this