[BioC] Odd warning in simpleaffy, using quality control

[Maciej Jończyk]

> The cdf package is installed and working. (I've been preprocessing 
> the
> same datafiles using 'affy') I still (almost) the same error:
>
> Attaching package: 'hugene10stv1cdf'
>
> The following object(s) are masked from 'package:hgu133plus2cdf':
>
>     i2xy, xy2i
>
> Error: NAs in foreign function call (arg 1)
> In addition: Warning message:
> In qc.affy(unnormalised, ...) :
>   CDF Environment name ' hgu133plus2cdf ' does not match cdfname '
> hugene10stv1cdf '
>
> I might have missunderstood something. Does the qc function in
> simpleaffy not recognize cdfName by itself, or do I have to specify
> it?

Hi David,

For me it seems that in R environment you have loaded hgu133plus2cdf 
and it persists after
installation of hugene10stv1cdf package.
 From simple.affy package:
"
qc.affy(unnormalised,normalised=NULL,tau=0.015,logged=TRUE,
cdfn=cdfName(unnormalised))
"

cdfn option:

"The cdf name for the array - can be used to specify a different set of 
probes to
     the default"

Maybe try to specify correct cdf using cdfn option.

HTH,
Maciej