Hey, Rohit -

I'm rusty on this, but my recollection is:

Scanalyze, a microarray image analysis package, produced foreground
(CH[12]I_MEAN) and local background (CH[12]B_MEDIAN) intensity values, but
not background-subtracted intensities (CH[12]D_MEAN), which were by somewhat
odd convention calculated by the Stanford Microarray Database (SMD) as mean
foreground minus median background:

    CH[12]D_MEAN = CH[12]I_MEAN - CH[12]B_MEDIAN

The different qualifiers, Scanalyze vs. SMD, indicate the origin of the
given value.

For signal values, you probably want the "SMD:RESULT.CH[12]D_MEAN" columns -
that's what was generally used for further analysis.  The rest of the
columns are mostly various QC metrics.  CORR is probably the most valuable
spot quality metric, indicating the cross-channel pixel-to-pixel correlation
(1 is good, 0 is very bad, 0.6 was the typical threshold I saw employed).
FLAG is set to a non-zero value if the user indicated a problem with the
spot, which might or might not be reflected in the other QC metrics.

Cordially,

- Jeremy


On Tue, Jun 8, 2010 at 11:39 PM, Rohit Farmer <rohit.farmer@gmail.com>wrote:

> Hi everyone ... i am trying to build an object using ArrayExpress package
> for an SMD data available at ArrayExpress using the following command
>
> data  <- ArrayExpress("E-SMDB-1428")
>
> but the object is not being created and m getting the following errors
>
> Error in nonAB(i, files, path, ph, rawcol, adr, adf, idf) :
>  2 scanner names are given ( "ScanAlyze" "SMD" ). It is not possible to
> handle such a case. Try to set the argument 'rawcol' by choosing among the
> following columns names:
> "ScanAlyze:RESULT.CH1I_MEAN"
> "ScanAlyze:RESULT.CH2I_MEAN"
> "ScanAlyze:RESULT.CH1B_MEDIAN"
> "ScanAlyze:RESULT.CH2B_MEDIAN"
> "SMD:RESULT.CH1D_MEAN"
> "SMD:RESULT.CH2D_MEAN"
> "ScanAlyze:RESULT.CH1B_MEAN"
> "ScanAlyze:RESULT.CH2B_MEAN"
> "ScanAlyze:RESULT.PERGTBCH1I_1SD"
> "ScanAlyze:RESULT.PERGTBCH2I_1SD"
> "ScanAlyze:RESULT.PIX_RAT2_MEDIAN"
> "ScanAlyze:RESULT.TOT_SPIX"
> "ScanAlyze:RESULT.TOT_BPIX"
> "ScanAlyze:RESULT.REGR"
> "ScanAlyze:RESULT.CORR"
> "ScanAlyze:TOP"
> "ScanAlyze:BOT"
> "ScanAlyze:LEFT"
> "ScanAlyze:RIGHT"
> "ScanAlyze:RESULT.FLAG"
>
> please help me to sort out this problem
>
> regards
>
> Rohit
>
> --
> Rohit Farmer
> M.Tech Bioinformatics
> Department of Computational Biology and Bioinformatics
> Jacob School of Biengineering and Biotechnology
> Sam Higginbottom Institute of Agriculture, Technology and Sciences
> (Formerly known as Allahabad Agricultural Institute - Deemed University)
> Allahabad, UP, INDIA - 211 007
> Ph. No. 9839845093, 9415261403
> e-Mail rohit.farmer@gmail.com
> Blog http://rohitsspace.blogspot.com
>
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>
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-- 
Jeremy Gollub
jeremy@gollub.net

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