Some literature would suggest that Both GAPDH and Beta actin are too variable across different tissue types. But If they work for me (in other words if they do not vary in my assays regardless of any hormones that I treat them with), then does it matter matter? And can I still use them as controls?
Yes, they're definitely still acceptable to use as controls, and people use both of them all the time. Some people have criticized GAPDH as a control, but a lot of labs still use it (ours included.) Unfortunately, there's no real "perfect" control gene; we just use the ones that we think are least likely to change. Occasionally, I'll run both GAPDH and b-Actin, and if they're the same relative to each other, I can be a little more confident that they're good choices for controls.
If you're sure that your control genes aren't changing, then you can certainly still use them as controls.
I've found this page to be a really good resource for qPCR:
http://www.dorak.info/genetics/realtime.html
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