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 > [[alternative HTML version deleted]]

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