[BioC] Problems with read.maimages

Philipp Pagel p.pagel at wzw.tum.de
Mon Dec 22 20:28:16 CET 2008

On Mon, Dec 22, 2008 at 10:48:50AM -0200, Priscila Grynberg wrote:
> ScanArray Express software to generate my files. I have a .csv and a .gpr
> file.
> My Targets.txt file is:
>   SlideNumber Name                                FileName  Cy3  Cy5
> Date
> 1          83   N1 CLB_Cy3_CL14_Cy5_13860883_18Dez2008.gpr  CLB CL14
> 2008/18/12
> 2          85   N2 CL14_Cy3_CLB_Cy5_13860885_18Dez2008.gpr CL14  CLB
> 2008/18/12
> The commands that I tryied were:
> RG <- read.maimages(targets$FileName, source="genepix")
> Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected
> RG <- read.maimages(targets$FileName, source="genepix", sep="\t")
> Erro em `[.data.frame`(obj, , columns[[a]]) : undefined columns selected

>  RG <- read.maimages(targets$FileName, source="scanarrayexpress")
> Erro em readGenericHeader(fullname, columns = columns, sep = sep) :
>   Specified column headings not found in file

Are these copy&pasted? I'm asking, because the messages are not the same and
contain spelling errors.

Anyway, the messages suggest that your gpr files do not contain
the column headings expected. According to the source code of
read.maimages, the expected columns for source 'scanarrayexpress'

G = "Ch1 Mean", Gb = "Ch1 B Median", R = "Ch2 Mean", Rb = "Ch2 B Median"

Have a look at your files and make sure these columns are
present. If they are not, you have to specify the columns to be
used yourself using source='generic' and the columns option.  See
?read.maimages for details.


Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany

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