[BioC] Limma read GenePix version 6 file

Ye, Bin binye at med.wayne.edu
Fri Oct 14 20:11:28 CEST 2005


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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