Hi Eric, Thanks for helping, now things are clear to me.
Regards Ankit On Fri, 15 Mar 2019 at 19:11, Eric Deutsch <[email protected]> wrote: > Hi Ankit, both strategies would likely work okay. I would prefer first > combining all your data with iProphet and then creating the library with > SpectraST. An issue to consider: if you combine several libraries that have > been processed or thresholded individually, the final FDR will be higher > for the combined dataset than the individual ones. This is because the > correct identifications will mostly be in common, but the false > identifications will be mostly different in the different experiments and > so they will accumulate. So combining everything first with iProphet will > give you a better understanding of your FDR. > > > > Regards, > > Eric > > > > > > *From:* [email protected] < > [email protected]> *On Behalf Of *Ankit Balhara > *Sent:* Thursday, March 14, 2019 11:47 PM > *To:* spctools-discuss <[email protected]> > *Subject:* [spctools-discuss] Combining the data on two tissues in one > library > > > > Hi, > > > > I have acquired the DDA and DIA data on various tissues, and trying to > build a spectral library by combining the DDA results of all tissues, that > can be used further for the DIA data analysis. I am trying two approaches- > one assay library generation with SpectraST and other using skyline to > build the library. Now, I confused, how should I proceed. > > > > Should I combine the peptideprophet results of various tissues by using > iProphet? > > Or, create assay libraries for each tissue separately using the SpectraST > and then import them separately in a common Skyline document? > > > > I would be very grateful for your help. > > > > Thanks in advance. > > -- > 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]. > 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]. 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.
