Multiplatform batch correction using combat

Question

[Devyani]

Hi, I wanted to analyze data from various micro-array platform such as agilent, rosetta/merk. Below is the link to the three platforms from which I want to analyze data. Only one platform has both test and control samples, rest have only test samples. Some of the established method I came across is combat, but I'm not sure if it can be done for cross platform like this. Any idea on whether combat can be used for batch effect removal? Thank you in advance.

Platform1 Platform2 Platform3

Answer 1

[WouterDeCoster]

You cannot remove a batch effect which is confounded/masked by your biological effect. If you compare test samples of platform A with controls from platform B you cannot figure out if the differences are biological or technical.

[Devyani]

Thank you for the reply. Since I am new to batch effect analysis, I am still trying to understand things. I am coming across multiple conflicting results when I try to address my question Some say I can do and some say I can't. I will get back to you when I am more clear. Thank you