Pvalue and fold change calculation

This software calculates Fold Changes and Pvalues.

The initial R code of this software has been written by Marie Tosolini in 2011. If the groups are larger than 15 the normality of the distribution is tested by Shapiro-Wilk and then a T test or Wilkoxon test is performed.

For FC calculation of log2 values, it is possible to remove the log2 transformation.

Version 1.4 computes goups means and SD.

Manual :

1- install R programming language.

2- unzip the software

4- copy your files in the “data” directory. Very important : avoid spaces or special characters in files names. The files must be formated as follows (an example is given with the soft) :

- txt or csv files with TAB separator

- first line : column names

- first column : probset names or gene names

- second column (optional) : definitions / comments : any number of comment columns are accepted

- next columns : numerical values with dot as decimal separator. The first columns must contain expression values for the controls. The last columns must contain expression values for the second group.

4- start R and load the software using the command <source("software_name.r">

5- processed files (whole file and significant Pvalues files) are in the “results” directory.

CAUTION : calculations are done by a R program. R does not like special characters in strings, so be carefull to avoid any special character such as "*", "/", "-" etc... or the computation will fail.

Very important : avoid spaces or special characters in files names.