I've microarrayed samples after a gene knock-down (KD confirmed by qRT-PCR to be 95%) with Affymetrix Gene 1.0 ST arrays and Biotique XRAY software. The problem is, that this well expressed gene does not show up among the differentially expressed genes. My suspicion is that the expression in the KD samples drops below the background and is therefore not recorded by the software. Absolute, unmodified intensitiy of the probe for this gene can be found and is significantly lower in the knock-down samples. Could anyone give me some tips on this or e.g. tell me how to get the results from genes which are expressed in one control and completely silenced in the other?
Edited by Baars01, 22 July 2011 - 01:43 AM.