Author: semor
Date: Wed Sep 5 16:00:48 2012
New Revision: 17461
URL: http://svn.gna.org/viewcvs/relax?rev=17461&view=rev
Log:
Added more text to describe the consistency testing approach.
Also includes a very basic point by point protocol for consistency testing.
This was proposed by by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00028.html
(Message-id:
<CAED9pY_YTDj8SX8crQu9on4LqA=pLzQwwyaz9kMLWD96xg-d0g@xxxxxxxxxxxxxx>)
This also follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
Modified:
trunk/docs/latex/consistency_tests.tex
Modified: trunk/docs/latex/consistency_tests.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/consistency_tests.tex?rev=17461&r1=17460&r2=17461&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Wed Sep 5 16:00:48 2012
@@ -24,7 +24,7 @@
\item[$F_{R_2}$] A consistency function proposed by \citet{Fushman98}.
\end{description}
-Different methods exist to compare tests values calculated from one field to
another. These include correlation plots and histograms, and calculation of
correlation, skewness and kurtosis coefficients.
+Different methods exist to compare tests values calculated from one field to
another. These include correlation plots and histograms, and calculation of
correlation, skewness and kurtosis coefficients. The details of how to
interpret such analyses are avaliable at the end of this section in Section
\ref{sec: Visualisation and data output}.
For more details on the implementation within relax, see:
@@ -254,16 +254,32 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Visualisation and data output}
+\label{sec: Visualisation and data output}
The rest of the script is used to output the results to 2D Grace files for
visualisation (the \uf{grace.view} user function calls will launch Grace with
the created files), and the output of the values into plain text files.
However, simply visualizing the calculated $J(0)$, $F_\eta$, and $F_{R_2}$
values this way does not allow proper consistency testing. Indeed, for
assessing the consistency of relaxation data using these tests, different
methods exist to compare values calculated from one field to another. These
include correlation plots and histograms, and calculation of correlation,
skewness and kurtosis coefficients.
+
+To complete the consistency testing analysis, the following steps are needed:
+
+\begin{itemize}
+\item Extract the $J(0)$ values at multiple magnetic fields.
+\item Join together the data from a pair of magnetic fields either by
pasting them as two columns of one file (approach A), or by dividing values
from a first magnetic field by values from a second magnetic field (approach
B).
+\item Make either a correlation plot (approach A), or an histogram of the
ratios (approach B).
+\item See if the correlation plot is centered around a perfect correlation
or skewed away (approach A), or if the values are centered around 1 in the
histogram (approach B). If yes, data from multiple magnetic fields is
consistent from one magnetic field to another. If no, data is inconsistent.
In the case where inconsistency arises, if data from more than two magnetic
fields is avaliable, more than one pair of data can be checked and the
inconsistent magnetic field data can be identified.
+\end{itemize}
An example of such an analysis is shown in Figure \ref{fig: consistency
analysis} below
\begin{figure*}[h]
\label{fig: consistency analysis}
\includegraphics[width=0.9\textwidth]{graphics/analyses/consistency_testing/consistency__J0_PSE-4.eps.gz}
-\caption[Example of consistency testing visual analysis]{Example of
consistency testing visual analysis. Relaxation data from three different
magnetic fields are compared. For each pair of magnetic field, a correlation
plot of the calculated $J(0)$ values (top) as well as an histogram of the
ration of calculated $J(0)$ values (bottom) are shown.}
+\caption[Example of consistency testing visual analysis]{Example of
consistency testing visual analysis. Relaxation data from three different
magnetic fields are compared. For each pair of magnetic field, a correlation
plot of the calculated $J(0)$ values (approach A, top) as well as an
histogram of the ration of calculated $J(0)$ values (approach B, bottom) are
shown. Data from \citep{MorinGagne09b} is used for the purpose of this
example.}
\end{figure*}
+As shown in Figure \ref{fig: consistency analysis}, the example data
displays both consistent and inconsistent data. In fact, data recorded at 500
MHz and 600 MHz are consistent together, whereas data recorded at 800 MHz is
not consistent with data recorded at 500 MHz nor 600 MHz. Since more than
two magnetic fields were used, this allowed the identification of the data
from 800 MHz as the inconsistent data, as data from 500 MHz is consistent
with data from 600 MHz, and vice-versa. In this particular example, this
allowed the authors to take special care with data at 800 MHz.
+
+This inconsistency of 800 MHz data is seen on the correlation plot (toop) by
a deviation from the dotted line (which represents the theoretical situation
when equal $J(0)$ values are extracted from both magnetic fields. It is also
observable in the histogram (bottom) where the ration of the data from two
magnetic fields is not centered around 0. In fact, there seems to be a
systematic shift of the calculated $J(0)$ values at 800 MHz when compared to
the two other magnetic fields. This is caused by a similar shift in the
experimental $R_2$ (transversal relaxation rate) data.
+
+For the 500 MHz and 600 MHz data pair, the data are centered around the
dotted line in the correlation plot (approach A, top left) as well as
centered around a value of 1 in the histogram comparing the ratios of values
from both magnetic fields (approach B, bottom left). Of course, there are
some outsider values even in the case of consistent data. There are caused by
specific dynamic characteristics of these spins and are different from
systematic inconsistencies such as depicted in the example above with the
data recorded at 800 MHz.
+
r17461 - /trunk/docs/latex/consistency_tests.tex