Hi David, Yes this is the file. Briefly, I would open it and after a few minutes once loaded in Chrome I filter using an iProphet cutoff of 0.7360 and a text filter for 478.99|480.99 modification (subscript checked on). Trying to display all entries, or attempting to export to a spreadsheet results in the error warning. I'm running another analysis currently with a 0.05 cutoff. What browser are you using?
Best, Adam On Friday, August 31, 2018 at 5:25:27 PM UTC-5, David Shteynberg wrote: > > Hello Adam, > > I have not been able to replicate the issue you observed on the file you > gave me. Are you sure that the file you posted is the one showing up with > the error? > > Thanks, > -David > > On Fri, Aug 31, 2018 at 2:03 PM, Adam Rabalski <[email protected] > <javascript:>> wrote: > >> Considering the size of the file, which editors/viewers do you use at ISB >> to open XML file in order to pinpoint a problem? I have re-run the analysis >> as I had 87 fractions and 10 of them were labelled with timestamps (occurs >> when XCalibur attempts to write a filename that already exists in a >> directory so it creates a new file with the date/time added on to it) so I >> changed these file names as I thought that this might be the problem >> because I could not view peptides beyond this fraction number but am still >> running into the same issue and have different "error with html display" >> pointing to different lines depending on how I filter the xml file. Would >> reducing the output size help here? The only thing that I can think of >> doing is increasing the PeptideProphet Probability filter to 0.05 from 0.00 >> (which I typically use) in order to reduce the number of entries written . >> >> On Thursday, August 30, 2018 at 1:03:24 PM UTC-5, David Shteynberg wrote: >> >>> The errors above suggest that the pepXML files are not parser compliant >>> and cannot be read. Sometimes this could be caused by bad characters in >>> the protein descriptions from the fasta database, you have to look at the >>> specific lines pointed to by the error messages to identify the exact >>> issue. If you can post your failing files and I can take a look. >>> >>> Thanks, >>> -David >>> >> -- >> 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.
