Within each slide, expression values for spots associated to the same gene symbol were merged in a similar weighted fashion.
Correlation values of intra-slide duplicate values for each patient sample (plasma and synovial fluid, n = 20) were plotted to illustrate the precision of measurements across the experiment.
The resulting frequencies were used to calculate a sliding average value for a 50 AA window, which was plotted in a chart (see additional file 1: Comparative plot of the average corrected entropy of a 50 AA sliding window along the protein sequence).
Agreement was relatively high overall, ranging from 0.67 to 0.75 for readings of whole slides and values of 0.80 for reads on the TMA.
The data thus obtained is of two types: The first data set consists of Slide Positive Rates (SPR) values (for two types of malaria P. vivax and P. falciparum) over 37 time points in the city of Chennai (as recorded by the Corporation) from January 2002 to January 2005.
The CGH data is displayed as averaged values for sliding 130 kb windows, in log2 scale.
Data from a total of 48 slides, containing the intensity values for the control and the signal channels as well as the flag values for present, absent or marginal spots was uploaded and sample attributes were defined.
In order to address which parts of the studied genes exhibit signals of evolving under positive selection, we used CRANN analysis calculating dn and ds values for sliding and overlapping windows along individual genes (Additional file 5) [ 47, 48].
The idea that cultural regeneration is a value-for-money way of providing support for cities has found its place as we slide towards recession.
For the peptides that had replications, their normalized values were averaged to produce a list of unique peptides with their normalized values for each slide.
OA score was calculated by multiplication of the grade and stage values for each slide.
