I am pooling together tumor samples of of 4 different histology from 4 GEO studies that are done on Affymetrix U133 Plus 2.0. I want to compare differential genes and between each tumor histology and blood.
Here are my proposed approaches
1. Use insilicoDB to get fRMA normalized expression sets for each study so that all study will have been normalized the same way (Description: http://bit.ly/1OMmRJx). Use COMBAT to remove batch effects. Then run limma to get DE genes for each tumor histology against the pooled blood data.
2. Pool together raw cell files from all studies, run RMA , then limma to get DE genes for each tumor histology against pooled blood.
Thank you very much!