[BioC] marray and gathering additional information from GenePix GPR file

[Daniel Brewer]

J.delasHeras at ed.ac.uk wrote:
> Quoting Daniel Brewer <daniel.brewer at icr.ac.uk>:
> 
>> Hi,
>>
>> I am new to the use of bioconductor, so bear with me.  I am using
>> GenePix as my image processing software for cDNA arrays.  As it is set
>> up there is an automated procedure that determines whether a spot should
>> be considered for further use, and it uses the Normalize column to
>> indicate this (value of 1 accept, value of 0 drop).  I would like to
>> filter out all the "bad" spots after normalisation.
>>
>> I use the following to read in the GPR files.
>>> mraw <- read.GenePix(targets=TargetInfo,name.Gb = NULL, name.Rb = NULL)
>>
>> mraw at maW, successfully gives the flag values, but the Normalize column
>> does not appear to be in the object.  Is there anyway to input this
>> information?
>>
>> Many thanks
>>
>> Daniel Brewer
>>
>> **************************************************************
>>
>> Daniel Brewer, Ph.D.
>>
>> Institute of Cancer Research
> 
> Hi Daniel,
> 
> You could try reading the gpr file with 'read.table' as a data frame,
> take the column you want from it, add it to your marray object and
> delete the data frame.
> 
> I don't use marray, I use limma, and I use the same procedure to import
> other columns I am interested in (in my case the SNR columns at the end
> of the gpr file, and perhaps the flags).
> 
> I hope it helps.
> 
> Jose
> 

Thanks for the suggestion, I am sure that would work.  I did find
another way round it by defining weights i.e.

> mraw2 <- read.GenePix(targets=TargetInfo,name.Gb = NULL, name.Rb = NULL, name.W="Normalize")

And that seems to work fine.  I am sorry if this is a simplistic
question but I am trying to filter the marrayRaw object by this column
but I am running into problems.  This is the approach:

> mraw2[mraw2 at maW == 1,] 
Error in mraw2[mraw2 at maW == 1, ] : (subscript) logical subscript too long

I think this is because maW is a long vector across all microarrays
whereas the first index is just across one array.  Anyway round this.
What I am aiming to do is create an marray object with only those spots
with the normalize column = 1.  Maybe genefilter is more suited to this.

Thanks

Daniel Brewer