[BioC] problems with hgu133a2?

[Dick Beyer]

I hope someone can help me with a strange problem with affy hgu133a2.

I have an affy array with minimum signal and 1st Qu. signal equal zero, but it seems OK from the RPT file from GCOS:

>all.raw1
AffyBatch object
size of arrays=732x732 features (4191 kb)
cdf=HG-U133A_2 (22277 affyids)
number of samples=1
number of genes=22277
annotation=hgu133a2

>summary(exprs(all.raw1))
  3002 13July05.CEL
  Min.   :    0.0
  1st Qu.:    0.0
  Median :  123.0
  Mean   :  273.0
  3rd Qu.:  221.0
  Max.   :23109.0

Here is part of the RPT file fro this array:

Report Type:	Expression Report
Date:          	02:46PM 02/03/2006
______________________________________________________________________

Filename:		3002 13July05.CHP
Probe Array Type:	HG-U133A_2
Algorithm:		Statistical
Probe Pair Thr:	8
Controls:		Antisense
______________________________________________________________________

Alpha1:		0.05
Alpha2:		0.065
Tau:		0.015
Noise (RawQ):	2.450
Scale Factor (SF):	1.000
Norm Factor (NF):	1.000
______________________________________________________________________

Background:
 	Avg: 74.13	Std: 1.66	Min: 69.90	Max: 78.70
Noise:
 	Avg: 4.41	Std: 0.20	Min: 3.80	Max: 4.90
Corner+
 	Avg: 92		Count: 32
Corner-
 	Avg: 4055		Count: 32
Central-
 	Avg: 6919		Count: 9
______________________________________________________________________

The following data represents probe sets that exceed the probe pair threshold 
and are not called "No Call".

Total Probe Sets:	22277
Number Present:	12285	55.1%
Number Absent:	9770	43.9%
Number Marginal:	222	1.0%

Average Signal (P):	485.3
Average Signal (A):	13.0
Average Signal (M):	53.0
Average Signal (All):	273.8

When this array is in amongst several others, some of which summary shows as having a non-zero min and others like the one above, then gcrma and rma give me weird errors:

rma(all.raw)
Background correcting
Error in density.default(x, kernel = "epanechnikov", n = 2^14) :
         need at least 2 points to select a bandwidth automatically

Am I doing something wrong or is there a problem with hgu133a2 in affy? I haven't seen this type of behavior before.  simpleaffy's qc function gives this 0% present calls and 0 average background.

Thanks for any help,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer