[BioC] reading arrays image analysed with spot

[Jean Yee Hwa Yang]

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
> 
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