Dear all, I'm running TPP v.4.4 rev 1, on W7 with Apache HTTP server 2.2 and ActivePearl 5.8.9 (I'm a biologist so please forgive me if I write any mistake about informatics/programming).
I've got 2 biological replicates of my experiments, each experiment include 13 fractions. I've also got 2 biological replicates for the correspondent controls, each of 13 fractions. .d files (Agilent) are located under localhost/wwwroot/ISB/data/ PLCb1interactome. I specify all my filenames 'cos I reckon this may be case sensitive to solve my problem. 1st biological replicate is named as: 20111201_PLCbinteractome_PLCb_01 .... 13 20111201_PLCbinteractome_pBB_01 .... 13 --> this is the control 2nd biological replicate is named as: 20111212_PLCb1interactome_PLCb1_01 .... 13 20111212_PLCb1interactome_pBB_01 .... 13 --> this is the control mzxml conversion, X!Tandem search, pepxml comversion went fine. I run PeptideProphet with these parameters: Probability 0, use accurate mass binning, clevel -c-1. Saved the file under data/PLCb1interactome/ as interact-PLCb1 (and 2).pep.xml or interact-pBB1 (and 2).pep.xml. Then I moved to the tab combine analysis, I selected interact-PLCb1.pep.xml interact-PLCb2.pep.xml and I run iProphet either with and without the option do not use number of sibling searches 'cos I just have Tandem outputs. The model compiles correctly, either the interact.iproph.pep.xml and .shtml open but there's no link to the statistical model eg. I cannot click neither on prob or iprob. Plus no NSE, NSM png images are generated. I understood that sub-folders may be a problem infact when I organized the files as data/PLCbinteractome/PLCb1/ I couldn't even open the shtml file, with the error "cannot find the file". The same happened when I tried to run InterProphetParser from the command line: I cannot click on iprob or prob to see the model, but at least the .png images were generated. What am I doing wrong? PS. I checked the pep3D and they look fine. I checked the PeptideProphet files and they look fine to me, either the statistic model. Any suggestion will be really appreciated!!!! Cheers, Manu -- 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.
