Single channel analysis of two-color agilent array using limma

Question

[pm2012]

Hello

I fairly new to limma for analyzing two-color microarray data. I am trying to analyze a somewhat unusually designed experiment. Here's the design:

Filename           Cy3          Cy5
File1                M_cont      M_cont
File2                M_10hr      M_10hr
File1                M_14hr      M_14hr
File1                P_cont      P_cont
File1                M_10hr      M_10hr
File1                M_hr      M_14hr

I am following the instructions on limma userguide chapter 12. However, I keep getting the following error after this step:

corfit <- intraspotCorrelation(MA, design)

Warning messages:
1: In statmod::remlscore(y, X, Z) : reml: Max iterations exceeded
2: In statmod::remlscore(y, X, Z) : reml: Max iterations exceeded

Please help!