Just tried loading the file using Firefox. Filtering with the modification and probability works fine, but trying to display all entries results in another XML parsing error.
Adam On Friday, August 31, 2018 at 7:02:58 PM UTC-5, David Shteynberg wrote: > > I would not recommend using the 0.05% cutoff. I was able to open your > file and apply same filters you applied. I am using Firefox browser. > Which version of the TPP are you using? > > Thanks, > -David > > On Fri, Aug 31, 2018 at 3:33 PM, Adam Rabalski <[email protected] > <javascript:>> wrote: > >> 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]> >>> 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]. >>>> 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. >>>> >>> >>> -- >> 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.
