[BioC] about citrus chip (update of xps)

[cstrato]

Dear all,

Does someone has an explanation why Affymetrix has added probesets w/o 
MMs to the Citrus.CDF file?

BTW, I have just uploaded a new version xps_1.4.9 (and xps_1.5.16) to 
BioC which allows to do "mas5" and "mas5calls" for the Affymetrix Citrus 
array by simply skipping the probesets w/o MMs.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



James W. MacDonald wrote:
> 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:
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>