[BioC] Limma read GenePix version 6 file

[Gordon Smyth]

limma has been well tested with GenePix 6 and there should be no problem. 
Specifying columns explicitly should not be required. If you believe 
there's a limma error, please give the code you used so that we can debug.

BTW, the columns that Saroj specified (all medians) can now be given as

    source="genepix.median"

Gordon

>Date: Fri, 14 Oct 2005 16:11:25 -0400
>From: "Ye, Bin" <binye at med.wayne.edu>
>Subject: Re: [BioC] Limma read GenePix version 6 file
>To: "Saroj Mohapatra" <smohapat at vbi.vt.edu>
>Cc: bioconductor at stat.math.ethz.ch
>
>It works! Thank you, Saroj!
>
>Have a good weekend!
>
>
>
>Bin
>
>
>-----Original Message-----
>From: Saroj Mohapatra [mailto:smohapat at vbi.vt.edu]
>Sent: Fri 10/14/2005 3:19 PM
>To: Ye, Bin
>Cc: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Limma read GenePix version 6 file
>
>Bin:
>
>Which function are you using for reading the data?
>
>If you are using the limma function read.maimages, then the function
>provides some extra arguments that can force it to read specific
>columns. The help file says:
>
>----
>  > ?read.maimages()
>
>columns: list with fields 'Rf', 'Gf', 'Rb' and 'Gb' giving the column
>           names to be used for red and green foreground and background
>           or, in the case of Imagene data, a list with fields 'f' and
>           'b'.  This argument is not usually specified by the user but,
>           if it is, it over-rides 'source'.
>-----
>
>Something like this might work:
>
>myRG = read.maimages(myGenepix6Files, columns=list(Rf='F635 Median',
>Gf='F532 Median', Rb = 'B635 Median', Gb='B532 Median'), ...)
>
>Also, there are other arguments (other.columns) in the function for
>reading more columns from the file.
>
>Hope it helps. Best,
>
>Saroj
>
>Ye, Bin wrote:
>
> >Hi,
> >
> >When I try to read the GenePix output file from GenePix 6, I got an 
> error as below:
> >
> >Error in "[.data.frame"(obj, , columns[[a]]) :
> >        undefined columns selected
> >
> >I suspect GenePix 6 have some new columns different than previous version:
> >
> >Block  Column  Row     Name    ID      X       Y       Dia.    F635 
> Median     F635 Mean       F635 SD F635 CV B635    B635 Median     B635 
> Mean       B635 SD B635 CV % > B635+1SD    % > B635+2SD    F635 % 
> Sat.     F532 Median     F532 Mean       F532 SD F532 CV B532    B532 
> Median     B532 Mean       B532 SD B532 CV % > B532+1SD    % > 
> B532+2SD    F532 % Sat.     Ratio of Medians (635/532)      Ratio of 
> Means (635/532)        Median of Ratios (635/532)      Mean of Ratios 
> (635/532)        Ratios SD (635/532)     Rgn Ratio (635/532)     Rgn R2 
> (635/532)        F Pixels        B Pixels        Circularity     Sum of 
> Medians (635/532)        Sum of Means (635/532)  Log Ratio 
> (635/532)     F635 Median - B635      F532 Median - B532      F635 Mean - 
> B635        F532 Mean - B532        F635 Total Intensity    F532 Total 
> Intensity    SNR 635 SNR 532 Flags   Normalize       Autoflag
> >
> >Can anybody help me out? We need to deal with GenePix data for our 
> experiment.
> >
> >Thanks in advance!
> >
> >
> >Bin