Hi Mike, Thank you very much for your quick reply!
I combined the two result files, in this way I got 240 results, but the same problem appeared again. Do you have any other suggestions for validator software that works well with Kojak? Thanks a lot, Gabriella On Monday, November 12, 2018 at 9:39:01 PM UTC+1, Michael Hoopmann wrote: > > 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:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *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). 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 [email protected] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
