[BioC] Re: How to read flag info from ImaGene output file

Gordon K Smyth smyth at wehi.EDU.AU
Fri Jul 16 06:03:36 CEST 2004

There is no ImaGene output column called "flags", it is called "Flag". 
See for example


> Hi Gordon
> Thanks for the response. I have another question.
> I am reading Imagene output files using read.maimages (Limma) or
> ImaGeneData$read (Aroma). The former can read both files simultaneously
> whereas the latter reads each file separately. I was using read.maimages
> until I found that I could not get the flag information from the data.
> At some point of pre-processing I need to exclude the spots with certain
> flag values associated with it (the flags are attached during image
> quantification). Suppose I would like to exclude all the spots with a
> flag value of more than 0.

To do that you need

myfun <- function(x) as.numeric(x$Flag <= 0)


> When I do this:
> myfun<-function(x) as.numeric(x$flags > 0)
> RG<-read.maimages(files,source="imagene",wt.fun=myfun)
> I get the message that it reads the images and then:
> Error in "[<-"(`*tmp*`,,I,value=numeric(0)) :
>          Nothing to replace with
> I know that the files specified in the variable 'files' does have flags
> with higher values than zero. Was there a problem during the reading? Is
> there any other way to find the flag information?
> Also, I found that ImaGeneData$read (Aroma) does include flag
> information in the returned object. But I would have to read the flags
> manually and conditionally insert NAs for the corresponding R,G values.
> Thanks and regards,
> Saroj

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