 
 
hello Jim:

Sorry too trouble you again.After I installed affy package1.23.6 and Biobase 2.5.6 the mas5 problem have solved.But I meet the similar problems when run mas5calls and gcrma package on Citrus chips,I think problem must be the NA in Citrus Chip,But I can find another way to filtering out low quality data.

Here are the partial R codes :
> library(affy)
> affydata<-ReadAffy("cp1-a.CEL")
> affydata
AffyBatch object
size of arrays=984x984 features (16 kb)
cdf=Citrus (30395 affyids)
number of samples=1
number of genes=30395
annotation=citrus
notes=

> mas5.eset<-mas5(affydata)
background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...done.
30395 ids to be processed
#work well!!no problems!!


> pa_calls<-mas5calls(affydata)
Getting probe level data...
Computing p-values
Error in FUN(1L[[1L]], ...)  : NA/NaN/Inf in foreign function call


> gcrma(affydata)
Adjusting for optical effect.Done.
Computing affinitiesLoading required package: AnnotationDbi
Error in matrix(NA, nrow = max(cbind(pmIndex,
mmIndex)), ncol = 1) :matrix: invalid 'nrow' value (too large or NA)

> sessionInfo()
R version 2.9.1 (2009-06-26) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh_CN.UTF-8;LC_MONETARY=C;LC_MESSAGES=zh_CN.UTF-8;LC_PAPER=zh_CN.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] citrusprobe_2.4.0   AnnotationDbi_1.6.1 gcrma_2.16.0       
[4] Biostrings_2.12.8   IRanges_1.2.3       citruscdf_2.4.0    
[7] affy_1.23.6         Biobase_2.5.6      

loaded via a namespace (and not attached):
[1] affyio_1.12.0        DBI_0.2-4            preprocessCore_1.6.0
[4] RSQLite_0.7-2        splines_2.9.1        tools_2.9.1    

Best.
                    YuduanDing

RE:

<jmacdon@med.umich.edu>" 
2009-09-02 22:56:01
 Re: RE  James about mas5
The problem with running mas5 on the citrus chip is that there are 25 
probesets that don't have any MM probes. Since the MM probes are used 
for both background estimation/subtraction and computation of the 
expression values this will be a problem for these probesets.

I have fixed the error you see in the devel version of affy, so if you 
want to run mas5 on these data you need to upgrade to the devel version 
of R, and then either get the corrected version of affy from the svn 
server, or wait a day or two and use biocLite() to get it. The version 
of the corrected affy package is 1.23.6.

Best,

Jim



 wrote:

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826






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