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