Hi, dear members, I want to know whether someone has microarray meta-analysis experience. In my research, as mentioned in my previous question "How many genes differentially expressed in microarray can be seen as normal?", I want to combine microarray from different platforms, one microarray experiement was set in the sexual development time course (sexual development induction 0h, 24h, 48h, 72h, 96h and 144h; 0h was set as a control) of Gibberella zeae, a plant pathogen; the other microarray experiment is about a transcription factor mutant, it means a transcription factor in the strain was deleted, and it didn't produce any sexual organ after induction, the control of which is the normal sexual development strain, and the mRNA of them were extracted after 72h sexual induction. I actually want to combine these two platform microarray datasets.
I know many people using meta-analysis in this kind of situation. Can I do meta-analysis like this:
First, I would select differetially expressed genes in the two microarray platform separately by comparsion the treatment with their control.
Second, I get the fold changs of each treatment compared with their control. In the case of time course, I would get them like this: fdc1=24h/0h,fdc2=48h/0h, and so on. In the other case of transcription factor mutant, because this mutant didn't product sexual organ, can I see it as a control like the 0h control in the first microarray platform, then the fdc would be equal to (the control that produce sexual organ/the mutant).
Third, I want to use SAS or other software to compare the difference between the fold chang (first only at 72h) between the two different microarray platform, is this meaningful?
If I can compare them like the above, I would compare with the other time course such as 24h,48h,96h,144h. In this way, I would get genes fold chang are differentially expressed.
I would also want to compare this aquired gene set with the genes selected in the first step, maybe I can use venn diagram to get the intersection of these different expression genes along with the different fold chang genes. Are this procedures correct? I hope any of you can give me some suggestions about meta-analysis? Thanks very much!