[BioC] Error with ImaGene out put file in limma

Gordon Smyth smyth at wehi.edu.au
Wed Oct 22 03:00:13 MEST 2003

Updating my previous reply ...

Is is possible that you have edited the Image output files by hand and 
removed the header lines? If so, have you also removed the trailing lines 
"End Raw Data" etc at the end of file? If you have, then you can read the 
data in yourself using the R command read.table() and assemble an RGList 
object for yourself. Obviously you have to do this yourself - limma can't 
support user-edited files.


At 07:34 AM 22/10/2003, Marcelo Luiz de Laia wrote:
>Hi people,
>I execute this step in limma and I have a error below:
> > RegianeSample <-
> > RegianeSample
>   SlideNamber     FileNameCy3    FileNameCy5  Cy3 Cy5
>1           1 lamina1BCYE.txt lamina1XDM.txt BCYE XDM
>2           2 lamina2BCYE.txt lamina2XDM.txt BCYE XDM
>3           3 lamina3BCYE.txt lamina3XDM.txt BCYE XDM
> > slides <- RegianeSample$FileName
> > RG <- read.maimages(slides, source="imagene")
>Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x),  :
>         attempt to set an attribute on NULL
>Our out put file is like this (in the original file, lines not is broken and
>names of fields is separated with tab):
>Field   Meta Row        Meta Column     Row     Column
>XDM/BCYE        1       1       1       1
>Gene ID Flag    Signal Mean     Background Mean
>Cal 1   1       3.5E+16 8.5E+02
>Signal Median   Background Median
>3.6E+04 8.3E+02
>Meta Row range of 1 to 4;
>Meta Column range of 1 to 2
>Row range of 1 to 32;
>Column range of 1 to 24;
>Flag is 1, 2 or 3;
>Please, any tip are welcome and/or one step by step to analyze imagene out
>put file in limma is very apreciate!

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