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","C H1D_MEDIAN","CH1I_MEDIAN","CH1_PER_SAT","CH1I_SD","CH1B_MEAN","CH1B_ME DIAN","CH1B_SD","CH1D_MEAN","CH2I_MEAN","CH2D_MEAN","CH2D_MEDIAN","CH2 I_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_RAT 2_MEAN","PIX_RAT2_MEDIAN","PERGTBCH1I_1SD","PERGTBCH1I_2SD","PERGTBCH2 I_1SD","PERGTBCH2I_2SD","RAT1_MEAN","RAT1N_MEAN","RAT2_MEAN","RAT2_MED IAN","RAT2_SD","RAT2N_MEAN","RAT2N_MEDIAN","REGR","SUM_MEAN","SUM_MEDI AN","TOT_BPIX","TOT_SPIX","X_COORD","Y_COORD","TOP","BOT","LEFT","RIGH T","CH1DL_MEAN","CH2DL_MEAN","LOG_RAT2L_MEAN","CH1DL_MEDIAN","CH2DL_ME DIAN","LOG_RAT2L_MEDIAN","SECTOR","SECTORROW","SECTORCOL","SOURCE","PL ATE","PROW","PCOL","FAILED","IS_VERIFIED","IS_CONTAMINATED","LUID)

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","C H2I_MEDIAN","CH2_PER_SAT","CH2I_SD","CH2B_MEAN","CH2B_MEDIAN","CH2B_SD ","CH2BN_MEDIAN","CH2DN_MEAN","CH2IN_MEAN","CH2DN_MEDIAN","CH2IN_MEDIA N","CORR","DIAMETER","FLAG","LOG_RAT2N_MEAN","LOG_RAT2N_MEDIAN","PIX_R AT2_MEAN","PIX_RAT2_MEDIAN","PERGTBCH1I_1SD","PERGTBCH1I_2SD","PERGTBC H2I_1SD","PERGTBCH2I_2SD","RAT1_MEAN","RAT1N_MEAN","RAT2_MEAN","RAT2_M EDIAN","RAT2_SD","RAT2N_MEAN","RAT2N_MEDIAN","REGR","SUM_MEAN","SUM_ME DIAN","TOT_BPIX","TOT_SPIX","X_COORD","Y_COORD","TOP","BOT","LEFT","RI GHT","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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]