Hi,

I am working on analysis of a publicly available two-channel Agilent data (GEO id: GSE43303).

Here the experiment design is as follows: Comparison of 630E strain 8h, 14h, or 38h of infection in vivo vs. 630E strain 8h in vitro.

Considering few raw files as examples:

GSM1060320 - VIVO8H1-cy3_VITRO8H-cy5; 
GSM1060321 - VIVO8H1-cy5_VITRO8H-cy3; 
GSM1060328 - VIVO14H1-cy3_VITRO8H-cy5; 
GSM1060329 - VIVO14H1-cy5_VITRO8H-cy3

It is clear that 8hr in vitro samples are considered as references in this experiment. However, I need expression values of 8hr in vitro samples for my analysis.

Since, taking the ratio of cy3/cy5 will give me a relative intensity of test condition with respect to the reference. Therefore, I would like to know, If I can take the intensity values of each channel (cy3 and cy5) separately for further analysis?

Thanks,