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

Jenny Drnevich drnevich at uiuc.edu
Fri Jul 7 16:42:48 CEST 2006

Hi Daniel,

>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.

First, I would caution you about discarding all spots called 'bad' by your 
GenePix setup - do you really know what it's doing? Often, spots are 
labeled 'bad' if the spot foreground is not detectable above some level of 
the background. Unless there is a defect on the chip, these type of spots 
are actually 'real' data, not 'bad' data - more like a value of 0. Now, the 
number that is associated with that spot is not entirely accurate, but it 
is relatively accurate compared to spots with detectable values. In an 
extreme example, by throwing out these spots, you may not detect a gene 
that is only turned on in one of your treatment groups! However, you do 
need to discard spot values that are a result of obvious defects on the 
array, so you still need an answer to your question:

You can't really 'remove' all the spots that have normalize=0 from the 
marray object because it has to be a full matrix. One possibility is to set 
them all to NA:

mraw2[mraw2 at maW==0] <- NA
# note there is no row,col in the subsetting because you want to replace 
individual values, not rows or columns

However, this may cause problems farther down the line if some functions 
can't handle NA values. I not really familiar with marray objects, but in 
limma RGList or MAList objects, having a spot weighted zero means that it 
will not be used in most functions automatically. You should check into how 
the preprocessing & analysis functions you want to use work - they may 
already make use of your maW component, or they may have an argument to set 
weights in the call to the function.


>Daniel Brewer
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
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e-mail: drnevich at uiuc.edu

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