[BioC] Design matrix in Combat algorithm

[Neagu Matei Stefan [guest]]

I am currently trying to use ComBat from sva package in order to eliminate the batch effect from some Ilumina data obtained in an experiment. I have read the article Adjusting batch effects in microarray expression data
using empirical Bayes method,W. EVAN JOHNSON, CHENG LI∗,ARIEL RABINOVIC but I did not understand very well how the elements in matrix X of the model Yijg = αg + Xβg + γig + δigεijg are obtained.
Could you please give me a better insight on this subject?

Thank you very much,
Neagu Matei Stefan

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Romanian_Romania.1250  LC_CTYPE=Romanian_Romania.1250   
[3] LC_MONETARY=Romanian_Romania.1250 LC_NUMERIC=C                     
[5] LC_TIME=Romanian_Romania.1250    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base  

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