[BioC] PLMset and image function

[James W. MacDonald]

Edwards.Stephen at epamail.epa.gov wrote:
> I tried reinstalling via biocLite("affyPLM"), and I still get the same 
> error.  Here is the information from traceback():
> 
>>traceback()
> 
> 4: stop("argument must be matrix-like")
> 3: image.default(Pset1, which = 2)
> 2: image(Pset1, which = 2)
> 1: image(Pset1, which = 2)

I think the problem here is you are ending up with image.default() being 
called on your PLMset instead of the image() function defined in 
affyPLM, which extracts a matrix of values and then feeds that to 
image.default().

What do you get if you just type Pset1 at an R prompt? Something like this?

Probe level linear model (PLMset) object
size of arrays=640x640
cdf=HG_U95Av2 (12625 probeset ids)
number of samples=
number of probesets=12625
number of chip level parameters for each probeset= 4
annotation=hgu95av2
PLMset settings
Creating function: fitPLM
Preprocessing
Background Correction=TRUE Method= RMA.2
Normalization=TRUE Method= quantile

Model/Summarization
$constraint.type
           default
"contr.treatment"

[snip]


> 
> Is there a cleaner way to reinstall a package rather than simply running 
> biocLite?  If so, I will try that.

That should be fine, as long as you do it using a fresh instance of R 
(and no other versions opened that might have affyPLM loaded).

Best,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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