Dear John, Have you read any documentation? The meaning of the components returned by lmFit() are described briefly on the help page help("MArrayLM-class") and more mathematically on Section 10.2 "Fitted model objects" in the limma User's Guide. Best wishes Gordon ------ original message ------- From: John Holden john.holden78@gmail.com Date: Sun Mar 21 00:49:23 CET 2010 Hi, I am not able to understand what R is doing in the background while calculating the $stdev.unscaled and $sigma values from using the lmfit() function for microarrays. Any ideas? Thanks in advance, John Holden ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}