Hi Edwin,
Did you ever get an answer to this? We always install Labkey/CPAS first
but would be nice to know the root cause.
DD
On Thursday, September 25, 2008 10:18:15 PM UTC-4, Edwin Lowe wrote:
>
> I mentioned this on the list a while ago. I have a problem with running
> CPAS 8.1 and the la
I found the msconvert of proteowizard is very convenient.
It comes with vendor reader, so I don't need to install xcalibur.
http://proteowizard.sourceforge.net/downloads.shtml
Maybe you can convert the RAW file to mzML before using TPP.
On Friday, November 23, 2012 11:07:39 PM UTC+8, Alex w
I am considering using target-decoy FDR or directly using E-value of
x!tandem?
It seems that xtandem author recommend the latter.
*(*
*This reference describes the idea of using reversed sequences to validated
large collections of protein identifications. The GPM has this method
built-in as a
Dear All (especially David),
I am trying to use the ANN retention time predictor. The training runs OK,
but when trying to use it I get this error:
gsl: init_source.c:29: ERROR: vector length n must be positive integer
Default GSL error handler invoked.
This application has requested the Runtim
Hi Magnus,
Can you forward me the files you have and the commands you are using and I
will debug?
Thanks,
-David
On Thu, Mar 28, 2013 at 10:47 AM, magnus.palmb...@gmail.com <
magnus.palmb...@gmail.com> wrote:
> Dear All (especially David),
>
> I am trying to use the ANN retention time predictor
OK - I sent the training set and the ANN model by e-mail.
On Thursday, 28 March 2013 18:49:41 UTC+1, David Shteynberg wrote:
>
> Hi Magnus,
>
> Can you forward me the files you have and the commands you are using and I
> will debug?
>
> Thanks,
> -David
>
> On Thu, Mar 28, 2013 at 10:47 AM, magnu
I found out my problem thanks to following the directions that Alex wrote.
I was lacking part of the Microsoft Visual C ++ 2010 Redistribution
package on the computer. Once I downloaded the file I needed
(MSVCP100.dll) from Microsoft, the file conversion in TPP worked just fine.
Thanks! Mar
Thanks for the files you've provided. I was able to find and fix one error
in the code. TPP revision 6171 from trunk should contain this fix. Also I
found an error in your commands. When you train a a Neural Net with RTCalc
you have to use the ANN= option if you want to then apply the trained m
Hi all,
I have a question about FDR estimation for protein identification (using
reversed decoy database together with target database in a single file).
I can estimate the probability threshold for peptides to get for example 1%
FDR. My question is how to use this peptide probability thre
Hi,
Interpretation of e-values will always be coupled to the database size
(more appropriately, the size of candidates for a particular spectrum). So,
I do not think it is the correct metric for controlling false positives.
When the authors had suggested using e-values, I believe FDR was not in u
Hi Pavel,
The choice of peptide-level FDR or protein-level FDR depends on what
conclusions you hope to make. If you want to make conclusions about the
peptides you have identified, you can use peptide-level FDR. If you are
trying to identify proteins for biological reasons you should use
pr
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