[BioC] about citrus chip

[James W. MacDonald]

Making any changes to mas5calls will be much less trivial than the 
background correction, and I don't have the time right now to spend on that.

Your best bet is to use rma() and then filter on something like IQR. See 
the genefilter package for more options.

Best,

Jim



yuduanding wrote:
>  
>  
> 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 at 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:
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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