
 p {margin-top:0px;margin-bottom:0px;} 





Hello Bioconductor users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />

We have carried the following experiment: two different fly strains (58 and 104) were tested (each) under two different conditions, Control and Pulse (C and P). For each strain, samples from two conditions were labelled with Cy3 and Cy5 and hybridized together to the same array. Two (biological) replicates were carried for each hybridization. 

We are interested in finding those genes for which the difference C-P is maximized (and significant) between the strains. In other words, we are interested in the difference of the differences: (C[58]-P[58]) – (C[104]-P[104]). 

The target file looks like that:

SlideNumber            FileName       Cy3     Cy5

1          58 UP1_LP1.gpr       control            pulse

2          58 UP2_LP2.gpr       control            pulse

3          104 UP1_LP1.gpr     control            pulse

4          104 UP1_LP1.gpr     control            pulse

 

Could anyone please help us with writing the design and contrast matrix for analysing this experiment with Limma?

 

Many thanks, Eran



Eran Tauber (PhD) 
Lecturer in Molecular Evolution 
Dept. of Genetics 
University of Leicester 
University Rd, Leicester LE1 7RH 
England 

	[[alternative(swapped) HTML version deleted]]

This is MIME Epilogue

