Commit 7b6dc83e authored by Olivier Langella's avatar Olivier Langella
Browse files

documentation : output results

parent 7f7d3336
......@@ -98,8 +98,8 @@
<quantification>
<quantification_results>
<quantification_result output_file="result1" format ="tsv"/>
<quantification_result output_file="result2" format="gnumeric"/>
<quantification_result output_file="result3" format ="xhtmltable"/>
<quantification_result output_file="result2" format="ods"/>
<compar_result output_file="compar" format="ods" />
<quantification_result output_file="result4" format ="masschroqml" xic_traces="true"/>
</quantification_results>
<quantification_traces>
......
......@@ -122,7 +122,7 @@
\def\sitemasschroq{http://pappso.inra.fr/bioinfo/masschroq/}
\newcommand{\Pa}{\emph{PAPPSO}}
\newcommand{\mcq}{MassChroQ}
\newcommand{\mcqv}{MassChroQ v.2.1}
\newcommand{\mcqv}{MassChroQ v.2.2}
\newcommand{\xtp}{\emph{X!TandemPipeline}}
\newcommand{\xt}{\emph{X!Tandem}}
\newcommand{\mexe}{\texttt{masschroq}}
......@@ -131,7 +131,7 @@
%\def \xtp {X!TandemPipeline}
%\def \xt {X!Tandem}
%\def \mcq {MassChroQ}
\def \version {2.1}
\def \version {2.2}
\theoremstyle{plain}
......@@ -1757,38 +1757,31 @@ format and name of the files that will contain the final
quantification results. The format can be :
\bi
\item \ttt{tsv} : tab-separated values text format; this format
is ready to use for automatic or manual statistical analysis ;
\item \ttt{gnumeric} : Gnome spreadsheet format to use with Gnumeric software;
\item \ttt{xhtmltable} : xhtml (eXtensible HyperText Markup Language)
format; all the results are in an xhtml table and you can visualize
them via an Internet browser for example;
is ready to use for automatic or manual statistical analysis ;
\item \ttt{ods} : Open Document Spreadsheet this format is easy to use directly in
your preferred office suite (LibreOffice or MS Office);
\item \ttt{maschroqml} : masschroqML format, XML format, used as an
input but also output format to MassChroQ; it is intended for development use,
for example to integrate masschroq results in databases.
\ei
The user can choose multiple output formats for the same analysis as
we have done in the example above. We have chosen to export results
into a tsv file that will be called \ttt{result1.tsv}, a gnumeric file
that will be called \ttt{result2.gnumeric}, etc.
into tsv files in a directory called \ttt{result1.d}, an ods file
that will be called \ttt{result2.ods}, etc.
the \ttt{compar\_result} writes in one tab all peptides quantification results with one column per MS run.
This output gives a quick overview of the differences between MS samples.
\begin{note}
The \ttt{tsv} and \ttt{xhtmltable} outputs
will create two files : one with extension \ttt{\_pep} containing the
quantification results, and a second one with extension
\ttt{\_prot} resuming for each peptide, the corresponding proteins and
descriptions. Both these files are well suited for automatical
statistical analysis. The \ttt{gnumeric} format will contain two separate
sheets for each of them. The \ttt{tsv} output will also create a third file with
the extension \ttt{\_compar}, containing the quantification results
sorted in a different way, well suited for a first direct visual
verification of the results.
The \ttt{ods} outputs will create a single file containing results in separate tabs.
The \ttt{tsv} outputs will create one directory with the given filename and the results
tabs are separated in different files.
The different tabs are :
\ttt{proteins} resuming for each peptide, the corresponding proteins and
descriptions.
One or several tabs begining with \ttt{peptides\_} followed by the quantification XML id.
It contains the quantification results.
\end{note}
In the example above three files named
\ttt{results\_pep.tsv}, \ttt{results\_prot.tsv} and
\ttt{results\_compar.tsv} will be created for
the tsv format and a unique file named \ttt{results.gnumeric}
containing two sheets for the \ttt{gnumeric} format.
\subsection*{Alignment result (\ttt{.time}) files}
When {\mcq} reads the \ttt{align} tag in its input masschroqML file (lines $57$
......
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