Hi, I want to analyze some gene expressions in human cancer sample, so I downloaded the raw CEL files from NCBI GEO from different GEO series(ie. GSE60697 and GSE9348). then i used RMA normalization for each series. and i found differences between samples from different series. like this:
X1 1007_s_at 1053_at 117_at 121_at 1255_g_at 1294_at 1316_at 1320_at 1405_i_at 1431_at 1 GSM358347 11.00181 8.44362 7.158441 9.215471 4.769039 7.664939 6.415506 6.180747 8.607589 4.830004 2 GSM1581701 10.01269 7.81094 5.572275 7.395991 2.884339 7.597989 5.883037 4.473780 7.194491 3.380647
I think every value in the second line is smaller then the first line. if i want to analyze expressions from different series in a "pooled" dataset, should i re-normalize it to housekeeper genes?