Thank you and I got it. Eileen ________________________________________ From: [email protected] [[email protected]] On Behalf Of Jimmy Eng [[email protected]] Sent: Thursday, Octhttps://mail.ohsu.edu/owa/?ae=PreFormAction&t=IPM.Note&a=Reply&id=RgAAAACoBXuKBY50So0M11W6QS0eBwAwORkwhez9Q6LQfxc5yy1aAAAAA%2ffPAAAET8RhI7%2fMTIMabRHOGGDDAAFjLrCoAAAJ#ober 27, 2011 2:34 PM To: [email protected] Subject: Re: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error
When you click on a protein ratio link, ASAPRatio appears to grab information from the prot.xml file whereas that link for xpress attempts to grab all related peptide entries from the pep.xml to display. I don't know ASAPRatio well enough to give you a better explanation than that. On Thu, Oct 27, 2011 at 2:21 PM, Eileen Yue <[email protected]> wrote: > Jimmy: > Thank you for your help! I will try to use ASAP ratio information for my data. > > By the way, I am just curious why xpress can not open and asap information > can be open. They both should have similar size on computer or ASAP may even > have more since it includes different charge quantification information. > > Thank you again for your kind help! > > Eileen > ________________________________________ > From: [email protected] [[email protected]] > On Behalf Of Jimmy Eng [[email protected]] > Sent: Wednesday, October 26, 2011 4:14 PM > To: [email protected] > Subject: Re: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error > > Eileen, > > I see the problem but I don't have a fix for your issue with that CGI > program that results from clicking on the protein xpress ratio. > There's a process that translates XML data to the resulting web page > that you were hoping to see when you click that link. The TPP uses a > program xsltproc to transform a pep.xml file to list out the search > entries that were quantified for a particular protein. On my linux > box, it took its time but ran through fine on your data. On my > windows PC, that xsltproc process used up to 2GB of memory and failed > with an out of memory error. I don't know if this out of memory error > is due to my 32-bit PC being low on memory (it has just 3GB of RAM) or > if it hit a 2GB memory cap for 32-bit applications. > > At this point, I guess I'd encourage you to simply use ASASPRatio. Or > attempt to run the TPP on a 64-bit box and possibly patch > c:\inetpub\tpp-bin\xsltproc.exe to access up to 4GB ram (see > http://bit.ly/o3fJTo). I don't know if the latter will work or not as > I don't use 64-bit Windows here. > > This belongs in the developers forum but anyone know if there's a good > alternative to xsltproc? I was able to manually do the transformation > using Xalan and memory usage was much less but it was slow. The > underlying pep.xml file being transformed is 338MB which caused xerces > to use up to 2GB. On my linux box, xerces consumed 2.1GB when it ran > to completion; it failed at just past 2.05GB on Windows. > > - Jimmy > > On Thu, Oct 20, 2011 at 2:14 PM, Eileen Yue <[email protected]> wrote: >> Hi Jimmy: >> After I tested one fraction, I run TPP for my 12 fraction together to >> analyze the xpress and Asap ratio. They run smoothly and completed after two >> days. >> >> There is similar problem like before but without any error information: I >> clicked the protein xpress ratio to see the all the peptide xpress ratio >> information, they only showed: >> >> <-- TPP v4.5 RAPTURE rev 0, Build 201109211427 (MinGW) --> >> XPressCGIProteinDisplay (TPP v4.5 RAPTURE rev 0, Build 201109211427 (MinGW)) >> XPRESS ratio in ProteinProphet: light:heavy (1.29 ± 0.46) >> sp|A0AV96|RBM47_HUMAN 6 entries used >> 1.29:1.00 >> 1.00:0.77 >> --------------------------------------------------------------------------------c:/Inetpub/wwwroot/ISB/data/ISL1026/isl_er/interact.pep.xml >> -------------------------------------------------------------------------------- >> Click RELOAD in your browser to re-evaluate ratio if changes have been made >> to the XPRESS quantitation in any of the entries above. This will update >> what you see in the current ratio just above. >> To accept the current ratio back to ProteinProphet, click on the button >> below. >> >> >> But when I checked the asap ratio, everything is fine. >> >> Do you know how I solve this problem? >> >> Thank you >> Eileen >> >> >> ________________________________________ >> From: [email protected] [[email protected]] >> On Behalf Of Eileen Yue [[email protected]] >> Sent: Tuesday, October 18, 2011 3:22 PM >> To: [email protected] >> Subject: RE: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error >> >> Hi Jimmy: >> Thank you so much and it works! I just tried one fraction and it works >> perfectly! >> >> So appreciate all of you for your kind help! >> >> Eileen >> ________________________________________ >> From: [email protected] [[email protected]] >> On Behalf Of Jimmy Eng [[email protected]] >> Sent: Tuesday, October 18, 2011 1:41 PM >> To: [email protected] >> Subject: Re: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error >> >> Eileen, >> >> Can you download the following executable and update your TPP binary >> with this one: >> >> http://proteomicsresource.washington.edu/dist/XPressPeptideUpdateParser.cgi >> >> The files should go in c:\inetpub\tpp-bin\. Let me know if this fix >> does not work for the problem you're experiencing. >> >> - Jimmy >> >> On Tue, Oct 18, 2011 at 10:51 AM, Eileen Yue <[email protected]> wrote: >>> Hi Joe: >>> I did convert mzml files. the problem is that the error showed up when I >>> click the xpress ratio in prot.xml files. If I open the pep.shtml and click >>> the xpress ratio, it is fine and showed me the chromatrography information >>> for this peptide. This will not work if I open the prot.shtml and click the >>> xpress ratio. The ASAP ratio is fine and I can open them and see the >>> chromatography information. >>> >>> Thanks >>> Eileen >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
