Dear Natalie and David,
I have examined the peptide IDs probabilities through pepXML viewer
and there are plenty of them with probability greater than 0.05. I
also ran xinteract specifying the -p0 flag, and again protein prophet
gives error. The command output is as follows:
[r...@localhost outp
Hi Amanda,
The error message says:
running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/
Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/18337.pep.xml""
file 1: c:/Inetpub/wwwroot/ISB/data/18337.RAW_analysis_test/
18337.pep.xml
processed altogether 0 results
This means there wa
Hi Dave,
Yes there is such a tool and its integrated into the latest version of
Petunia user interface. Are you using commandline based TPP or are
you running Petunia?
Thanks,
-David
On Mon, Dec 15, 2008 at 1:43 PM, Dave @ UPENN wrote:
>
> Good Evening,
>When a decoy database is used with
Hello Dave,
We have no on-going efforts to integrate Crux, but are always open to make
the TPP compatible with as many search strategies as possible. So yes,
please let us know when you have tidied up your changes, and we can
coordinate on integrating them into the code.
Cheers,
--Luis
On Fri,
Hi Dave,
You may need to use the -d X flag if your decoy proteins don't begin
with the DECOY_ string. See calctppstat.pl --help.
The negative numbers are there as flags representing N/A. To successfully
get stats for P<0.001, you need to run xinteract with -p0 flag, which you
probably didn
Hello Amanda,
Please try the latest release, 4.1.1 (November) instead of 4.0.2 (July), as
many bugs have been fixed. Perhaps this issue has already been addressed.
Best wishes,
Natalie
On Mon, Dec 15, 2008 at 2:51 PM, Amanda wrote:
>
> I'm trying to run Protein prophet but keep running into
I'm trying to run Protein prophet but keep running into the same
error.
So far, I started with a .RAW file (290MB) and converted it to both
mzXML (667Mb) and mzML (1GB). I then did a Database search and got
the
expected folder with .dta files (2852 files, 1-15KB each). I
converted these to a .pep
Hello,
I am currently using a decoy database with xinteract and noticed
that some of the statistics appear to be incorrect. Has anyone else
experienced this?
Decoy results:
PP Incor P>0.9=30
Decoy IDs at P>0.9=0
Decoy IDs at P<0.001=-1
Total IDs at P<0.001=-2
Decoy fraction P<0.00
Good Evening,
When a decoy database is used with xinteract, is there any way to
see the empirical error rate through protein prophet or peptide
prophet?
Thanks,
Dave
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And just to confirm, I do *not* see any differences in mzXML files using my
4.1.1 TPP installation, either converting from the web interface or from the
windows command-line.
-Natalie
On Mon, Dec 15, 2008 at 12:44 PM, Natalie Tasman wrote:
> Also, can you verify that the same version of ReAdW i
Also, can you verify that the same version of ReAdW is being called in both
version? Please check that the only version of readw on your system is in
C:\Inetput\tpp-bin (using Windows "find files") and let us know. Maybe one
of your tests is using an older version?
Natalie
On Mon, Dec 15, 2008
I can see where that would work for the most part: the only difference
would be if lexical_cast (in pwiz, optimized to use strtod instead of
iostream) is locale-agnostic or not, i.e. will it parse a double with a
comma in it as a decimal place? My guess would be it does, but it's a
good thing
Hi all,
In a previous post, I was mentioning that Libra is not writing the
quantitation output to the peptide and protein reports.
I have been advised to update to the latest version. I have done that,
but still libra is not producing any quantitation output.
Any help will be appreciated.
Thanks
Hello Malick and Brian,
We have a clue as to what may be going on, thanks to Luis and Brian's
detective work. Brian had previously posted that the filter lines looked
different between the two files.
It's interesting to see some differences in the mzXML file beyond the
missing peaks:
filterLine
Hi Logan,
thanks for the macports update! If you specify full paths in
tpp_gui.pl configuration the www user running Apache2 should be able
to execute the binaries. I wouldn't change system wide paths. Make
sure the binaries are executable by everyone.
Cheers,
Ulrich
On Dec 15, 2008, at 9
Perhaps I spoke too soon, I have one more problem yet to be resolved.
Can anyone tell me how to change the system-wide PATH variable on OS X
10.5? The Web GUI runs as some user other than myself, so the TPP
binaries are not in its path and it can't run any commands (but if I
copy and paste the sa
Hi all,
Sorry for the delay on this. It appears that the gui (Petunia) was
installed correctly along with all the TPP binaries, I did not need to
change any other paths or config files for that. I had one problem
with the GUI, as follows:
When I logged in, I got an MD5_GEN error on the Home pa
It wouldn't be any different in IPP, it uses the same readw.exe (and in any
case, TPP receives much more active support so we should concentrate on
that) - did you check into the multiple thermo DLL possibility discussed
below?
-Original Message-
From: spctools-discuss@googlegroups.com
[m
Dear Brian,
I used the same commandline params readw -v --mzXML in commandline.
What did you received for the same source file in IPP
Regards from Malick
On 12 dec, 19:45, "Brian Pratt" wrote:
> >> Could it be that included Xcalibur .dll files in TPP don't match ?
>
> The TPP doesn't inclu
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