Hi, I used Limma to analyze microarray data. I have a question with M value. Is it correct that M value correspond to Log2(Signal in Cy5) - Log2(Signal in Cy3)? So if the difference equal to zero, it means that there is no difference beetween two sample. I want to know how to have a "true" fold value with the M value ? I mean if I have M Value = -4.685278 it mean that we have a difference beetween Cy5 and Cy3 intensity log2 value, so that "gene" is over expressed in Cy3 but with which value, 2 times, 3 times, 6 times.....? So in fact my question is how to transform the M value, in over expressed value ? Then i can compare this over expressed value with the value obtain in RT PCR Real Time. Thanks. Eric.

> Is it correct that M value correspond to Log2(Signal in Cy5) - > Log2(Signal in Cy3)? yes. > So in fact my question is how to transform the M value, in over > expressed value ? Just do some basic math: M = log2(Cy5) - log2(Cy3) M = log2( Cy5/Cy3 ) 2^M = Cy5/Cy3 cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel