Hi Gabriella, I’m not an expert on Percolator (or machine learning) but I think the problem is simply that the dataset is too small. There are only 128 results, which need to be split into training and cross-validation test sets, and thus there isn’t much data to train or test the models. Manually looking at the results show some PSMs to be highly likely to be correct, but Percolator requires a lot more PSMs to perform its analysis correctly (a limitation of this type of validation approach).
An option you have would be to combine your intra and inter protein Kojak results into a single dataset to give Percolator. Likely, you have a lot of intra-protein PSMs. Both of these result sets have the same parameters for Percolator and thus they can be combined, even if it is not the most ideal approach. Combining intra and inter protein PSMs can be done with cut-and-paste in Excel or a text editor. Just make sure you have only one header line at the top of the file. Cheers, Mike From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com] On Behalf Of Gabriella Gellen Sent: Thursday, November 08, 2018 7:15 AM To: spctools-discuss Subject: [spctools-discuss] Percolator stopped working using Kojak result files Hi Everyone, I'm quite new to Percolator and now I am practicing with data, that has already been published to have crosslinks using Hekate ( <https://www.ncbi.nlm.nih.gov/pubmed/24010795> https://www.ncbi.nlm.nih.gov/pubmed/24010795). I am trying to validate the crosslinked results found by Kojak 1.6.1 using Percolator 3.02. However, the program stopped working, and I got no results. It says "Warning: No target-decoy protein pairs found for the picked protein strategy. Check if the correct decoy pattern was specified with the -P flag; if the target protein is called "protA" and the decoy protein "decoy_protA", use the option "-P decoy_"." But the settings for the decoy pattern were correct. What do you think can be the problem for this? Thank you for your help in advance, Gabriella -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
