#8 Out of range error

[SASI MANNE]

Hi,
I am running saintq on my input files and getting the following error "St12out_of_range vector".

I have created the input .tsv file with protein intesities and the params file similar to the ones in the example folder.

Can i get help in formating my inputs properly so that i can run this succesfully ?

Find attached my param file and input file.

Thank you
Sasi

[Hyungwon Choi]

Hi, your NS_LFQ.tsv file contains protein and "peptide" labels even though the parameter file says "protein level" analysis. So you need to remove either the first or the second column in the NS_LFQ.tsv file. I just tested with your sample file and it works. Let me know if this doesn't work for you.
HC

[SASI MANNE]

Hi,
Thankyou for the quick reply,i removed the second column and tried rerunning and i am still getting the same error,did u have to change anything else in the paramter file or the input file?

Thank you
Sasi

[Hyungwon Choi]

Not really, I just removed one column. I'm attaching the input and output files.

Hw

[Hyungwon Choi]

One thing I would do is to set "normalize_control=true" instead of false. Attaching the input and output again.

[SASI MANNE]

Thank you Hyungwon,i will try.

[SASI MANNE]

I wanted to know which version worked and on which OS,i used the same input files on MacOSx and using saintq_v0.0.4,still getting this error,do u have any suggestion to fix this

[Hyungwon Choi]

I'm not too sure. Your data works on mine, both on mac and linux after removing the peptide column. The only thing I can suspect is the new line character difference, even then we addressed this issue in the code.

[SASI MANNE]

The input format was not unix compatible which was causing the error,it is fixed now.

Your manual at http://crapome.org/sites/default/files/bi0815.pdf helped.

For future reference

"Reopen tab-delimited files generated from Mac OS X or Microsoft Windows in a text editor in a Unix environment and re-save as Unix-compatible tab-delimited files. The Unix utilities mac2unix and dos2unix may be used for this purpose. Alternatively, open each file in a nano text editor, press Ctrl+O once for saving, and keep pressing Esc+D until the file type shows neither [DOS format] nor [MAC OS format] next to the file name. Hit the Enter key to save."