[BioC] Error with ImaGene out put file in limma

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Tue Oct 21 23:34:08 MEST 2003

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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