Here's some tips on how to use the web-base RED-T applet (version 1.x)
(Note: this is not the RED-T application. This is the older version of this GUI which is available in a web-dependant applet form.)
How to load a protein
Type in the name of the text file, which needs to be in a ASCII format and press the LOAD button. (note: for a successful activation of the LOAD button, please click the button with a short hold).
If the file is in another subdirectory or location, the full path must be entered for a successful load.
The formats are in the form x-axis-name"_"y-axis-name. For example, avg_013.txt plots the x-axis with avg and y-axis with whatever 013 is... Most of the formats available so far for analysis, are avg_013.txt... which plots the average of the controls vs. protein/cluster #13.
Intra-domain analysis
In order to analyze within each group, i.e. Bacteria with Bacteria, or Proteobacteria within themselves, use the tree box in the lower left corner. Highlight or click your choice from the taxonomic hierarchy available in a tree format.
Inter-domain analysis
In order to analyze across each group, i.e. Archaea with Bacteria and/or Eukaryotes, use the two tree boxes in the lower right corner. Highlight or click your choice from the taxonomic hierarchy available in a tree format in each box. Both boxes must have a selection in order for a cross domain comparison to be illustrated.
Other things to know:
Drag&Highlight - any desired plot(s) can be highlighted using a mouse drag and drop operation: simply left click and hold while dragging from left to right the area of the plot(s). Upon completion, release the left mouse button. The resulted green boxed will highlight the desired plot(s) and the calculated values will reflect only these plot(s).
Highlight mode - when this box is selected, all plots are displayed in a bland background color. What ever comparisons you choose with this selected will display the plots in a yellow color. (note: if a plot is not visible, it could be due to its presence in a high concentration of plots, thus it is recommended to zoom the plot area of plot by decreasing the x and y plot range.
Identify Plots - click the "Get Data" button at the bottom of the page (below the applet), and the plot's label and coordinates (x,y) is displayed in a mini-window. This content of this window can be cleared by clicking on the "clear" button.
Refresh Graph - this button needs to be pressed when the graphs axis ranges are changed
Calculated values - the number of comparisons (n), mean, standard deviation, relative standard deviation are calculated and displayed on the left side of the applet. Two numbers are calculated: value of the visible/selected comparisons "out of" the value of the total comparisons
Best-fit line and its slope value - when this box is selected, a best-fit line is drawn for the chosen plots. The slope of this line is also shown on the left side of the applet. When this option is not selected the slope value is null.
last modified: February 2001