hi,

i am doing analysis for 10 breast cancer arrays (two color Agilent4x44
arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
biological replicates ,means all 10 arrays have been prepared from 10
different patients.
there are two categories as nod negative and nod positive.Five arrays from
nod negative(5 patients) and five are from nod positive(another 5
patients).I want to see the differentially regulated genes between two
categories(NOD NEGATIVE vs NOD POSITIVE).
i designed the target file as given below..I want to make it sure whether it
is correct or not.

SampleNumber                 FileName         Cy3              Cy5
1                                      1135_NN.txt
wt1                 mu1
2                                      2157_NN.txt              wt1
        mu1
3                                      3159_NN.txt
wt1                 mu1
4                                      4171_NN.txt
wt1                 mu1
5                                      5179_NN.txt              wt1
                mu1
6                                      628_NP.txt
wt2                 mu2
7                                      758_NP.txt
wt2                 mu2
8                                      880_NP.txt
wt2                 mu2
9                                      993_NP.txt
wt2                 mu2
10                                   1096_NP.txt
wt2                 mu2

1 to 5 are nod negative and ,6 to 10 are nod positive.

thanx.
NEERAJ RANA
JRF
IISC BANGLORE(INDIA)

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