I'm quite new in bioinformatics and struggle with the following problem:
I want to detect significantly different expressed genes in a microarray data set downloaded from GEO. The Affymetrix microarray they used (Human Genome U133 Plus 2.0 Array) measures some genes several times (with different target oligonucleotides). I'm now wondering how to handle this data in the final statistical analysis. Do I have to:
1) keep all measurements until after the statistical analysis (t-test + multiple comparison correction)? If so, how do I handle genes that are significantly different expressed only once (but they are measured several times)? And if all measurements show a significant difference, which fold change do I choose for further analysis?
2) remove all measurements for one gene except one? How do I decide which one to keep and which ones to remove?
Thanks a lot in advance for your help on this matter. Also let me know if something needs further clarification.