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.
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