Dear Hua Weng,

You should probably check whether your regular spacing data is indeed regular spacing. Try a few grep("genename", RG$genes[,"Name"]) and check if the spacing is identical between spots

Because the correlation value is larger after sorting, I think that the spacing or layout you're using without ordering is not correct.
 
Jan Oosting 

>Dear Oosting and Dr. Smyth:
>
>After I tried my regular spacing microarray data, I found that the common coefficient after order with spacing =1 is different >from the coefficient with original spacing without order. And the difference is big, the first one with order is 0.5618, the >second one without order is 0.1711. Also the B-statistics based on first one is only half of the value of the B-statistics of the >second one. Could you be kind enough to tell me why this happens and is there some other good way can solve this irregular >spacing problem?
>
>Thank you very much,
>
> 
>
>Hua Weng




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