[BioC] Odd warning in simpleaffy, using quality control

[ejulia]

Maciej Jończyk <mjonczyk at ...> writes:

> 
> > 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
> 
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> 

Dear all, in particularly Maciej and David,

I'm wondering if you could help me.  I've been having about the kind of problems
as David's initial email mentioned.

Following Maciej's advice I installed cdf environments and tried to specify them
when calling qc.affy(), but I'm still stuck - see below for the relevant
commands from my R consule.

> D.Affy.qc<-qc.affy(D)
Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at",
"AFFX-HSAC07/X00351_M_at",  : 
  subscript out of bounds
In addition: Warning message:
In qc.affy(D) :
  CDF Environment name ' hgu95av2cdf ' does not match cdfname ' drosgenome1cdf '

> D.Affy.qc<-qc.affy(D, cdfn="DrosGenome1")
Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at",
"AFFX-HSAC07/X00351_M_at",  : 
  subscript out of bounds
In addition: Warning message:
In qc.affy(D, cdfn = "DrosGenome1") :
  CDF Environment name ' hgu95av2cdf ' does not match cdfname ' drosgenome1cdf '

> D.Affy.qc<-qc.affy(D, cdfn="hgu95av2cdf")
Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at",
"AFFX-HSAC07/X00351_M_at",  : 
  subscript out of bounds 

> D
AffyBatch object
size of arrays=640x640 features (28 kb)
cdf=DrosGenome1 (14010 affyids)
number of samples=36
number of genes=14010
annotation=drosgenome1
notes=

Any further suggestions would be very appreciated.
Also, if you there's any other package that could compute 
percent present and scale factor for me,
that'd do it.

With thanks and best wishes
Julia