Methylation normalization between samples from different platform
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2.3 years ago
9521ljh ▴ 50

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?

gene • 416 views
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2.3 years ago
ATpoint 64k

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.

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sincerely really thank you!!!

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