Oh, no I'll wait till the final release. thanks,
Brian > On Feb 19, 2014, at 6:58 PM, Joseph Slagel <[email protected]> > wrote: > > I normally put that up when we do the release. The RC4 email wasn't meant > for the mailing list -- I meant to send it to someone that was going to do > one final release before putting it out. If you want I can put a source > tarball up on the development folder. > > -Joe > > > >> On Wed, Feb 19, 2014 at 3:30 PM, Brian Hampton <[email protected]> wrote: >> Hi Joe, >> >> I only see the Win binaries. Is the source available yet? >> >> Brian >> >> >> >> >>> On Wed, Feb 19, 2014 at 4:19 PM, Joseph Slagel >>> <[email protected]> wrote: >>> You'll find the latest release candidate (RC4) in: >>> >>> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ >>> >>> Since I don't expect any more changes this should be effectively 4.7. >>> >>> -Joe >>> >>> >>> >>>> On Tue, Feb 18, 2014 at 10:28 PM, Robert Jones <[email protected]> >>>> wrote: >>>> Bjorn, >>>> >>>> Thank you so very much that was extremely helpful! I'll be well on my way >>>> to finishing my analysis. >>>> >>>> -Robert M Jones >>>> >>>> >>>>> On Tuesday, February 18, 2014 6:45:24 AM UTC-7, Bjorn wrote: >>>>> Hi, >>>>> As far as I understand it, the TPP uses a mixture model-based approach to >>>>> determine posterior probabilities and it then uses these probabilities to >>>>> estimate the FDR. This can be done with or without the use of a decoy >>>>> database. However, when using some of the more sophisticated options >>>>> (like non-parametric modelling), you will need a decoy database to help >>>>> the modelling algorithms pin down the negative distribution. Also, when >>>>> the data is of not so excellent quality, the decoys can help make a >>>>> better distinction between good and bad identifications. >>>>> >>>>> After the analysis with ProteinProphet, you get something like this in >>>>> the ProteinProphet window: >>>>> >>>>> Prob Sens FPER Corr Incorr >>>>> 0.00 1.000 0.930 217 2874 >>>>> 0.10 1.000 0.337 217 110 >>>>> 0.20 1.000 0.337 217 110 >>>>> 0.30 0.915 0.216 198 55 >>>>> 0.40 0.865 0.152 187 34 >>>>> 0.50 0.816 0.102 177 20 >>>>> 0.60 0.777 0.074 168 14 >>>>> 0.70 0.747 0.058 162 10 >>>>> 0.80 0.647 0.019 140 3 >>>>> 0.90 0.608 0.010 132 1 >>>>> 0.95 0.569 0.005 123 1 >>>>> 0.96 0.547 0.004 119 0 >>>>> 0.97 0.529 0.003 115 0 >>>>> 0.98 0.507 0.002 110 0 >>>>> 0.99 0.470 0.001 102 0 >>>>> 1.00 0.152 0.000 33 0 >>>>> >>>>> The FPER is your FDR, so if you decide to set it at 1%, you notice that >>>>> this corresponds with a probability cut off of 0.90. Now, in your protein >>>>> list, you accept all proteins with a prob. of 0.09 or higher, which is >>>>> estimated to be 132 correct ones and 1 incorrect protein. Everything >>>>> below is discarded. >>>>> >>>>> I found lots of info in the following papers (esp. the last paper). >>>>> Hope this helps! >>>>> Cheers, >>>>> Bjorn >>>>> >>>>> [1] Choi, H., Fermin, D., and Nesvizhskii, A. I. Significance analysis of >>>>> spectral count data in label-free shotgun proteomics. Mol. Cell. >>>>> Proteomics 7, 12 (2008), 2373–2385. >>>>> >>>>> [2] Choi, H., Ghosh, D., and Nesvizhskii, A. I. Statistical validation of >>>>> peptide identifications in large-scale proteomics using the target-decoy >>>>> database search strategy and flexible mixture modeling. J. Proteome Res. >>>>> 7, 1 (2008), 286–292. >>>>> >>>>> [3] Choi, H., and Nesvizhskii, A. I. False discovery rates and related >>>>> statistical concepts in mass spectrometry-based proteomics. J. Proteome >>>>> Res. 7, 1 (2008), 47–50. >>>>> >>>>> [4] Choi, H., and Nesvizhskii, A. I. Semisupervised model-based >>>>> validation of peptide identifications in mass spectrometry-based >>>>> proteomics. J. Proteome Res. 7, 1 (2008), 254–265. >>>>> >>>>> [5] Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., >>>>> Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J. K., >>>>> Martin, D. B., Nesvizhskii, A. I., and Aebersold, R. A guided tour of the >>>>> Trans-Proteomic Pipeline. Proteomics 10, 6 (2010), 1150–1159. >>>>> >>>>> [6] Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. >>>>> Empirical statistical model to estimate the accuracy of peptide >>>>> identifications made by MS/MS and database search. Anal. Chem. 74, 20 >>>>> (2002), 5383–5392. >>>>> >>>>> [7] Nesvizhskii, A. I. A survey of computational methods and error rate >>>>> estimation procedures for peptide and protein identification in shotgun >>>>> proteomics. J. Proteomics 73, 11 (2010), 2092–2123. >>>> >>>> -- >>>> 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 http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >>> -- >>> Joe Slagel >>> Institute for Systems Biology >>> [email protected] >>> (206) 732-1362 >>> -- >>> 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 http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >> >> -- >> 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 http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > -- > 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 http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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