[BioC] simpleAffy, custom chip error

[Wittner, Ben, Ph.D.]

Hi,

I'm having the same problem as the person in the post below, namely, a call to
qc() fails with the message
"Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type:
xyzcdf",
even though the cdf environment for the custom chip could be loaded (as was done
successfully by rma() and expresso()).
Since I don't have the probes for the chip, it makes sense that 3'/5' ratios
would not be calculated, but could just that fail and other things such as
present/absent still go forward?

I also tried the package affyQCReport because in its manual it says "Any valid
AffyBatch object can be used as long as the corresponding CDF environment is
also available.", but it failed with the same message.

Thanks in advance.

-Ben

p.s., I'm running R 2.3.0 and BioC 1.8 release with simpleAffy version 2.6.0 on
platform i686-pc-linux-gnu.

----------------------------------------------------------------------------

Hi,
Simpleaffy needs various parameters to calculate the qc values properly
- these include the names of the probesets used to calculate 3'/5'
ratios and so on etc. These data are stored in the package, so aren't
available for your custom array. The error message you're getting is
because the package can't find them ...

I'll send another (longer) post later when I've worked out the best way
for you to get these data in... :-)
Cheers,

Crispin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Hilmar Lapp
Sent: 21 June 2005 01:11
To: Bioconductor
Cc: John Walker
Subject: [BioC] simpleAffy, custom chip error

Hi,

aside from Affy's commercial arrays we also use custom arrays, for which
we built the cdf and probe packages in order to be able to analyze them
with Bioconductor.

So far the custom arrays and their packages have worked fine, e.g. 
using gcRMA (just.gcrma()). However, they result in an error with
SimpleAffy (which works fine with Affy's commercial arrays). The error
message seems to indicate that the respective cdf and probe packages
aren't present ("I'm sorry I do not know about chip type: 
gngnf1musacdf"), but as a matter of fact they are. Issuing

	> library(gngnf1musacdf)

before the qc() call has no effect (i.e., it itself succeeds, but
doesn't help qc() succeed).

Below is a pertinent transcript. R is v2.0.1 and simpleaffy is v1.3.2.

Does anyone have any idea what's going on or how to track down the root
cause, and possibly even how to fix the problem?

	-hilmar