Methylation normalization between samples from different platform

Question

[9521ljh]

hello

i have SARCOMA methylation data from BeadChip platform.

and i found normal methylation data samples in TCGA from Illumina Human Methylation 450.

in minfi package, i try to read data to normalization. However, the error occurs because of different data format.

in this case , how can i normalize it?

Answer 1

[ATpoint]

You cannot. Platforms are too different to be used in the same statistical analysis. Results would be dominated by batch effects rather than biological truth.

[9521ljh]

sincerely really thank you!!!