Hi I am starting to work with cDNA chips from array comparative hybridization. I have severel arrays image analysed with spot 2.0, but the parameters (Excel Columns reported) are quite different from the ones in swirl.spot in the marray package, which has the command read.Spot. There are the following parameters in the Excel sheet. Can anybody help me further on how to read them in in a proper way? I would like to normalize them in different ways, but first I need to have the two channels in R. Furthermore the genes were spotted in triplicates. Is there a way to tell that in marray or any other package too? Thank you very much Arr-rowy Spot-colx Spot-rowy Flag nfore nback DapiFore DapiBack Dapi TestFore TestBack Test RefFore RefBack Ref Log2Rat RawRat SpotCorr MinF-B Slope Log2Slope TestIntercept RefIntercept OriginDist MeanLog2Rat MeanRat MedianRatio Log2MedRat

Hi Is this arrayCGH? I am guessing from your array output that it was analyzed with UCSFSpot which is not the same as Spot (produced by CSIRO). You may find some functions in the package "aCGH". Alternatively, you can use the function read.marrayRaw and specified the columns you considered red/green foreground or background. Cheers Jean On Thu, 20 Jan 2005, Auer Michael wrote: > Hi > > I am starting to work with cDNA chips from array comparative > hybridization. I have severel arrays image analysed with spot 2.0, but the > parameters (Excel Columns reported) are quite different from the ones in > swirl.spot in the marray package, which has the command read.Spot. There > are the following parameters in the Excel sheet. Can anybody help me > further on how to read them in in a proper way? I would like to normalize > them in different ways, but first I need to have the two channels in R. > Furthermore the genes were spotted in triplicates. Is there a way to tell > that in marray or any other package too? > Thank you very much > > Arr-rowy > Spot-colx > Spot-rowy > Flag > nfore > nback > DapiFore > DapiBack > Dapi > TestFore > TestBack > Test > RefFore > RefBack > Ref > Log2Rat > RawRat > SpotCorr > MinF-B > Slope > Log2Slope > TestIntercept > RefIntercept > OriginDist > MeanLog2Rat > MeanRat > MedianRatio > Log2MedRat > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Auer Michael wrote: >Hi > >I am starting to work with cDNA chips from array comparative >hybridization. I have severel arrays image analysed with spot 2.0, but the >parameters (Excel Columns reported) are quite different from the ones in >swirl.spot in the marray package, which has the command read.Spot. There >are the following parameters in the Excel sheet. Can anybody help me >further on how to read them in in a proper way? I would like to normalize >them in different ways, but first I need to have the two channels in R. >Furthermore the genes were spotted in triplicates. Is there a way to tell >that in marray or any other package too? >Thank you very much > >Arr-rowy >Spot-colx >Spot-rowy >Flag >nfore >nback >DapiFore >DapiBack >Dapi >TestFore >TestBack >Test >RefFore >RefBack >Ref >Log2Rat >RawRat >SpotCorr >MinF-B >Slope >Log2Slope >TestIntercept >RefIntercept >OriginDist >MeanLog2Rat >MeanRat >MedianRatio >Log2MedRat > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >