Is this something else and suppose to be a new post?
YP
On Jun 30, 11:08 am, "Zhi Sun" wrote:
> Hi all,
>
> I just checked in two programs, and did not put the log message.
>
> I will give a short description here:
>
> createChargeFile.pl: this program reads the ms2 file generated by CPM
> (cha
Can you be more specific? While some files have changed, and some have been
added, the source code directory structure is pretty much the same.
Brian
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Andreas Quandt
Sent: T
Hey Natalie, hello Brian
Sorry for getting back to you so late.
I tried the compilation and it worked like a charm :-)
I am only a little bit confused about the structure as it completely
differs from the stable branch.
Hence I am not exactly sure how to best integrate the trunk in an
existin
David--
Thanks. That's how I've been using it and the results have looked
really good.
Jake
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Hi Jake,
It is up to you to define the experiment boundaries. I would imagine
that different fractions of SCX of a single sample, for instance, can
be classified as one experiment. As long as different fractions or
separate physical runs have different MS data file names there will be
no proble
David--
Thanks for your reply. Just to clarify: if one wants to use iProphet
to combine physically separate analyses (eg., multiple SCX fractions
or gel slices, with a separate MS/MS data file for each) from a single
biological 'experiment'/sample, should the -E label be used to
differentiate ea
Hi Christine,
We do have a tool in the TPP, called iProphet, for combining search
engines. This tool applies a set of 5 statistical models of which the
search engine combining is merely one. We will have a paper coming
out on iProphet in the near future. Meanwhile, the tool is available
to try
Thanks, I'll have to play around with it some to see how I like it. I do
combine search engines, so it'll be interesting to compare the difference.
On Tue, Jun 30, 2009 at 1:41 PM, David Shteynberg <
dshteynb...@systemsbiology.org> wrote:
>
> One mistake to run ProteinProphet on iProphet dat
One mistake to run ProteinProphet on iProphet data you must use
the IPROPHET option as follows:
> ProteinProphet interact.iproph.pep.xml interact.iproph.prot.xml IPROPHET
On Tue, Jun 30, 2009 at 11:39 AM, David
Shteynberg wrote:
> Hi Greg,
>
> The iProphet powerful tool that is very simple
Hi Greg,
The iProphet powerful tool that is very simple to run. Unless you are
testing the performance of the various models iProphet applies, there
is not need to set iProphet parameters. The easiest way to run the
tool is on a single analysis (one experiment, one search engine),
this only req
Hi all,
I just checked in two programs, and did not put the log message.
I will give a short description here:
createChargeFile.pl: this program reads the ms2 file generated by CPM
(charge prediction program), or directory which contains a list of dta file,
and creates a .charge file. The .cha
Hi,
I am trying to run the xinteract on the omssa pep.xml output files. my
omssa's version is 2.1.4, my TPP version is 4.2.1. But I couldn't get
it through. I search the old post, there is a similar post, but the
problem was solved by specifying enzyme to xinteract.
I tried it, but is still not
Just bumping this one up, since it looks like it got missed.
On Jun 10, 12:08 pm, "bowers...@gmail.com"
wrote:
> I was wondering if someone could post some more detail on iProphet.
> One thing that I would like to know is what all command line arguments
> it takes, maybe some sample command line
Hello Johannes,
I hope that other people on the list will chime in with their advice,
but to start things of, here is a link to the official X!Tandem
reference on all available parameters and options:
http://www.thegpm.org/TANDEM/api/index.html
Note that some of these options may be specifi
Hello Petri,
If you're interested in mzXML, I would recommend starting here:
http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML
Regarding mzXML tools, you'll find information on data converters
which take vendor-specific files and convert them to mzXML as well as
other tools.
Hello Oded, Hello James, Hello Group,
could you please give me some advice how i can create a x!tandem
parameters file? is there any way to do this except from changing the
xml-code of the example files?
thank you a lot for the help!
Johannes
On 26 Jun., 22:13, James Dowell wrote:
> Oded,
>
>
Hello,
I have some questions concerning protein groups derived from
ProteinProphet. The questions seem to be independent of recent TPP
versions (they arise as well with TPP v4.1 as with TPP v4.2). OS is
linux.
To illustrate my questions I have uploaded three XML extracts from two
different experi
Hi
I would like to know what processing options I have for mzXML data
format in TPP. I tried to look for this from
http://sourceforge.net/projects/sashimi/
but it didn't catch my eye. Could somebody with more experience point
me to a right direction or even better, tell me?
Thank you,
-Petri
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