EdgeR issue for normalization of count reads

usegalaxy.eu support
#1

i have 28 samples each containing gene Ensembl IDs and read counts. i want to use edgeR to normalize to TPM here on galaxy but when i load my data and run it the following error appears.

Fatal error: Exit code 1 ()
Error: Sample IDs in factors file and count matrix don’t match

please i need help to resolve this problem

1 Like
#2

This may seem obvious, but review the Sample IDs in both inputs and make sure they are a match.

Be sure to not start IDs with numbers – and use only alphanumeric characters (a-z, A-Z, 0-9), dashes, and underscores in the names.

Also check for the following, some which may look “hidden” when viewing the datasets (“whitespace” characters):

  1. inconsistent capitalization
  2. blank fields, internal or at the end of lines
  3. blank lines
  4. extra or trailing spaces/tabs

The first three you’ll need to fix yourself, before uploading the data to Galaxy or sometimes using Text Manipulation tools within Galaxy (you’ll need to experiment).

The last can often be remedied by using the “convert spaces to tabs” option in the Upload tool.

upload-settings-spacestotabs

Let’s start there, and the EU team can jump in if problems persist.

Thanks!