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

Saroj Mohapatra saroj at wayne.edu
Thu Jul 15 20:35:59 CEST 2004

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. 

When I do this:

myfun<-function(x) as.numeric(x$flags > 0)

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,


-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Wednesday, July 14, 2004 6:34 PM
To: saroj at wayne.edu
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Difference between normalizeWithinArrays and stat.ma

Print-tip loess normalization in limma is identical to that in sma
(deliberately).  However the limma command accommodates weights while
stat.ma() does not.

I like sma but it is a no longer under development.  Better to use one
the BioC packages under active development and support such as marray or


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