[BioC] layout cDNA in limma

[Srinivas Iyyer]

Dear group, 

I downloaded raw data from UNC genome center. 

These are agilent ver 1 chips (from Chuck Perou's lab). (GSE686). 
looking at header they appear to be smd.old format. (header names given below as comma sep).

when I read RG file:

RG <- read.maimages(files,source="smd.old")

> RG$genes[210:335,1:4]
    SPOT   NAME                    Clone ID Gene Symbol
210  210 562084 AGILENT_HUMAN1_CDNA_1987205   HUMGT198A
211  211  EMPTY                                        
212  212 562085 AGILENT_HUMAN1_CDNA_3369232       KLRC4
213  213 562086 AGILENT_HUMAN1_CDNA_1853369        GAS7
214  214 562087 AGILENT_HUMAN1_CDNA_1833976       TCF12
215  215 562088 AGILENT_HUMAN1_CDNA_5264385      ZNF345
216  216 562089 AGILENT_HUMAN1_CDNA_4310857       KCNH3
217  217 562090 AGILENT_HUMAN1_CDNA_3015811       NET-2
218  218 562091 AGILENT_HUMAN1_CDNA_1888962    FLJ11040
219  219  EMPTY                                        

> RG <- backgroundCorrect(RG,method='normexp',offset=50)
> MA <- normalizeWithinArrays(RG,layout=RG$genes,method="printtiploess")
Error in if (nprobes2 != nprobes) stop("printer layout information does not match M row dimension") : 
  argument is of length zero

Now I do not have typical block and spot coordinates for these chips. 
How can I get layout object. Am I missing something or files missing something. I appreciate if any can help me here. 
thanks
Srini





(SPOT","NAME","Clone ID","Gene Symbol","Gene Name","Cluster ID","Accession","Preferred
 name","EXPTID","SPOT","SUID","PRINTID","DATE_MODIFIED","CH1I_MEAN","CH1D_MEDIAN","CH1I_MEDIAN","CH1_PER_SAT","CH1I_SD","CH1B_MEAN","CH1B_MEDIAN","CH1B_SD","CH1D_MEAN","CH2I_MEAN","CH2D_MEAN","CH2D_MEDIAN","CH2I_MEDIAN","CH2_PER_SAT","CH2I_SD","CH2B_MEAN","CH2B_MEDIAN","CH2B_SD","CH2BN_MEDIAN","CH2DN_MEAN","CH2IN_MEAN","CH2DN_MEDIAN","CH2IN_MEDIAN","CORR","DIAMETER","FLAG","LOG_RAT2N_MEAN","LOG_RAT2N_MEDIAN","PIX_RAT2_MEAN","PIX_RAT2_MEDIAN","PERGTBCH1I_1SD","PERGTBCH1I_2SD","PERGTBCH2I_1SD","PERGTBCH2I_2SD","RAT1_MEAN","RAT1N_MEAN","RAT2_MEAN","RAT2_MEDIAN","RAT2_SD","RAT2N_MEAN","RAT2N_MEDIAN","REGR","SUM_MEAN","SUM_MEDIAN","TOT_BPIX","TOT_SPIX","X_COORD","Y_COORD","TOP","BOT","LEFT","RIGHT","CH1DL_MEAN","CH2DL_MEAN","LOG_RAT2L_MEAN","CH1DL_MEDIAN","CH2DL_MEDIAN","LOG_RAT2L_MEDIAN","SECTOR","SECTORROW","SECTORCOL","SOURCE","PLATE","PROW","PCOL","FAILED","IS_VERIFIED","IS_CONTAMINATED","LUID)