Hello,

I am wondering what the best way is to merge the data produced by affy and agilent. I used limma to read arrays and to get normalized data, but they are different in data distribution. After using zscore for all two arrays and removing batch effect, the data seemed even for all of them. Any suggestion would be appreciated.

Best,

Jphn  

Rather than merging data, you might have better luck doing a meta analysis.
 

Dear John,

i used recently the R package  inSilicoMeging (http://www.bioconductor.org/packages/release/bioc/html/inSilicoMerging.html) to merge two affymetrix datasets i had of different platform-hgu133a & hgu133plus2-. The package performs merging regarding the common probesets and also performs batch effect correction regarding the different studies. I'm not sure about the complete different technology you intend to combine, but you could search the vignette, paper(http://www.biomedcentral.com/1471-2105/13/335) or adress the authors with a message regarding this specific matter.

Best,

Efstathios