[BioC] reading background from imagene output

[Gordon Smyth]

At 02:27 PM 23/03/2004, Matthew Ritchie wrote:
>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"))

Matt,

That's not quite right. You need

RG<-read.maimages(files, source="imagene", columns=list(f="Signal 
Mean",b="Background Mean"))

As the help says:

  columns: list with fields 'Rf', 'Gf', 'Rb' and 'Gb' giving the column
           names to be used for red and green foreground and background
           or, in the case of Imagene data, a list with fields 'f' and
           'b'.  This argument is not usually specified by the user but,
           if it is, it over-rides 'source'.

Can I leave you to correct it on the list?

Cheers
Gordon

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