[BioC] Limma read GenePix version 6 file

Ye, Bin binye at med.wayne.edu
Fri Oct 14 22:11:25 CEST 2005

It works! Thank you, Saroj!

Have a good weekend!


-----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

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,


Ye, Bin wrote:

>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!
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