p value for this example should be just under .95, p value of 0.9 that you were using will give you 2.1% FDR. I almost always run MAYU on my results and that tells the p Value corresponding to 1% FDR at protein level.
On Wed, Mar 20, 2013 at 3:40 PM, Sandeep <[email protected]> wrote: > Thanks for you answer. I want to make sure my calculation is correct. The > details of protein prophet result is - > > *Minimum probability**Sensitivity**Error rate*0.00 1.00000.89600.101.0000 > 0.23900.201.00000.23900.300.96700.17800.400.9410 0.14600.500.90700.1170 > 0.600.86300.08900.700.80800.06400.800.73900.0420 0.900.62900.02100.95 > 0.52100.00900.960.50100.00700.970.47400.00600.98 0.41300.00300.990.3690 > 0.00101.000.08600.0000 > > > Based on this result, what is > probability cutoff that gives me 1% FDR? > > Thanks > > Sandeep > > > > > > On Friday, March 15, 2013 11:01:24 AM UTC-5, kshitiz wrote: > >> Sorry I probably was not clear enough. Number of unique peptides for a >> protein are actually number of PSMs, so hypothetically if a protein was >> identified based on one peptide that was fragmented 10 times and 8 out of >> those 10 ms/ms spectra result in peptide spectrum match , then number of >> unique peptides will read 8 however you have identified only one peptide. >> >> I hope someone on the forum can correct me if I am wrong. >> >> Additionally, you said that you filter at p > 0.9, this is not very >> informative and not the best way of filtering. Instead you should filter at >> a p value that controls for less than 1% FDR. >> >> cheers >> >> >> On Fri, Mar 15, 2013 at 3:05 PM, Sandeep <[email protected]> wrote: >> >>> Hello, >>> >>> Sorry, I think I did not understand your answer. My concern was- why I >>> have more number of unique peptides as compared to TOTAL number of peptides >>> in my data after protein prophet grouping and filtering my data to contain >>> only groups with probability more than 0.9. >>> >>> Thanks >>> >>> Sandeep >>> >>> >>> >>> >>> On Friday, March 15, 2013 3:41:11 AM UTC-5, kshitiz wrote: >>>> >>>> Hi, >>>> I think the number given under number of unique peptides is actually >>>> number of unique PSMs used for the identity of that protein. If you want >>>> actual number of unique peptides then you will have to pull the data into >>>> an SQL based server and then query it to to count distinct peptides for >>>> each protein. >>>> >>>> cheers. >>>> >>>> >>>> On Thu, Mar 14, 2013 at 10:00 PM, Sandeep <[email protected]> wrote: >>>> >>>>> Hi, >>>>> >>>>> I have recently started using peptide/proteinprophet. I noticed that >>>>> in my data, there are several protein groups for which the number of >>>>> unique >>>>> peptidees is more than the number of total peptides (mostly the total >>>>> number of peptides is 0). Is this data reliable? How to explain this. >>>>> Thanks in advance for any answers. >>>>> >>>>> Sandeep >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 spctools-discu...@**googlegroups**.com. >>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>> Visit this group at http://groups.google.com/**group** >>>>> /spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>>>> . >>>>> For more options, visit >>>>> https://groups.google.com/**grou**ps/opt_out<https://groups.google.com/groups/opt_out> >>>>> . >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Kshitiz Tyagi >>>> >>>> -- >>> 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 spctools-discu...@**googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.**com. >>> Visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>> . >>> For more options, visit >>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>> . >>> >>> >>> >> >> >> >> -- >> Kshitiz Tyagi >> >> -- > 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?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- Kshitiz Tyagi -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
