Hi All

I know this question is asked previously many time. But i am facing some different issues . I have CEL file of Clariom S and U133 a2 affymetirx chip. CDF file for Clariom S is not available. I want to do meta-analysis of this data. I tried VirtualArray but its not working in my system. Is there any way i can do normalization putting all together the data generated from both the chip.

I also have normalised value (obtain separately ) of both chip. But it giving me huge difference For example.

Gene     Cl1          U1        U2         U3      U4
ABC     2.0         -10       -20        -15     -17

This data is from same(The data is from any of this phases that is 1 2 3 4 phase because same sample is processed with Clariom S. But the exact phase is unfortunately unknown ) . Here Cl1 is clariom sample and U1-U4 is u133 samples. Also I do not have control Based on this data we need to design internal control samples This data is phase wise data for example Phase 1 , 2, 3,4 Four phase are from U133 chip. I want to know my Clariom data is falling in which phase . Sorry i can not reveal exact details of samples that what this phases mean

Any help will be high appreciated !