I am working with 8 different microarray datasets comprising both
Illumina arrays to perform Meta-Analysis or Cross-Platform Analysis and identify biomarker signatures between
disease vs control condition.
I downloaded each dataset (
*.soft file from NCBI GEO dataset) individually and then sequentially processed by applying "
Quantile Normalization" followed by
Probe to Gene Mapping. The final dataframe/matrix will contain "
Gene Symbols" as
rows and "
columns for each dataset. Hence, all the 8 individual datasets were processed similarly irrespective of the array platform.
I have a question, since, the *.soft/series matrix file from NCBI GEO contains already normalized/log2 normalized data (all 8 datasets of interest were normalized/log2 normalized). Please let me know if it makes sense to re-normalize the data again using "Quantile Normalization" to accomplish meta-analysis or cross-platform analysis?