[BioC] reading background from imagene output

[Matthew Ritchie]

Hi Emanuele,

>Hello everybody,
>I've noticed that read.maimages doesn't read the same type of value for the signal and the background. If I'm not wrong Imagene output file has three values for them(mean,median and mode); apparently by default read.maimages takes the mean for the signal and the median for the background...
>
Correct.

>For example, how can I extract the median signal and the median background?
>I tried not to use the parameters source="imagene" and I've defined the columns of desired values:
>
>>RG<-read.maimages(files,R="Signal Mean",Rb="Background Mean",G="Signal Mean",Gb="Background mean")
>>
>
>but I got this message:
>
>Error in read.maimages(files, R = "Signal Mean", Rb = "Background Mean",  : 
>        Cannot find column heading in image output file
>
You're on the right track, however you haven't specified the 'columns' 
argument correctly in read.maimages().  The following should work.

>RG<-read.maimages(files, source="imagene", columns=list(Rf="Signal Mean",Rb="Background Mean",Gf="Signal Mean",Gb="Background mean"))
>

Best wishes,

Matt Ritchie

>please somebody help me out!
>sorry if once again I bother You with my basic questions...
>Thanks in advance.
>
>Emanuele
>

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