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eran tauber
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@eran-tauber-3712
Last seen 10.5 years ago
Hello Bioconductor users,
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]) â
(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
____________________________________________________________
Phone: 44 (0)116 252-3455, 252-3421 (lab) Fax: 44 (0)116 252-3378
www.le.ac.uk/genetics/et22
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