On Tue, Nov 18, 2008 at 6:57 PM, Srinivas Iyyer
<srini_iyyer_bio@yahoo.com>wrote:

> 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
>
>
Srini,

You might want to read the help for the PrintLayout-class.  I think you will
need to be able to construct that object before printtiploess will work.
Otherwise, use loess instead.

If you are asking what the layout for the array is, you might need to write
to the authors to get that information if is not available in the files that
you have.

Sean



>
>
>
> (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)
>
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