Microarray batch correction method suggestions

Question

[Sumeet]

Hi All,

I am working on minimum 10 different datasets of microarray, which combines of Affymetrix, Agilent, illumina etc. All data is pre-processed and log2 transformed. I would like to perform the analysis combining all data together. I applied limma batch-effect removal method, however, this method didn't really work. As far as I understand I can't use combat on negative values. So I was wondering if any one could suggest a approach to remove batch correction.

Thank you in advance

[ATpoint]

This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysis strategy.

[Sumeet]

Thank you ATpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.

[ATpoint]

Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.