Hello James,

I have tested as you mentioned below:

> nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf")))
Loading required package: AnnotationDbi

[1] 34901

This number is exactly the same as in the CDF file and matches with that of
RMA.

I get 34901 rows when I process single CEL file.  However, when I do
justRMA with 350 CEL files, number of rows in the output are 23068. Why
would this happen?

Please advise.

Thank you

Bhargavi

On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Bargavi,
>
>
> On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote:
>
>> Hello,
>>
>> I am using justRMA for processing 350 CEL files. When I does with RMA I
>> get
>> 34901 probe intensities  which match the CDF file. However, when I run
>> justRMA, I get only 23068 probe intensities. I am not sure why would this
>> happen?
>>
>
> It shouldn't, and we have done extensive testing to ensure that the
> results from justRMA() are identical to rma(). As an example:
>
> > nrow(exprs(rma(ReadAffy(**cdfname = "mogene10stmmrefseqcdf"))))
> Background correcting
> Normalizing
> Calculating Expression
> [1] 28312
> > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf")))
> [1] 28312
>
> So I get the same number of rows using both methods. Now check that I get
> the same exact values:
>
> > all.equal(exprs(rma(ReadAffy(**cdfname = "mogene10stmmrefseqcdf"))),**exprs(justRMA(cdfname
> = "mogene10stmmrefseqcdf")))
> Background correcting
> Normalizing
> Calculating Expression
> [1] TRUE
>
> So it looks OK to me.
>
> Best,
>
> Jim
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0
> [3] mogene10stv1cdf_2.11.0       AnnotationDbi_1.20.3
> [5] affy_1.36.0                  Biobase_2.18.0
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.26.0         BiocInstaller_1.8.3   DBI_0.2-5
>  [4] IRanges_1.16.4        parallel_2.15.1       preprocessCore_1.20.0
>  [7] RSQLite_0.11.2        stats4_2.15.1         tools_2.15.1
> [10] zlibbioc_1.4.0
> >
>
>
>
>> Below is the code I am using:
>>
>> library(affy)
>>     setwd('/home/run/testcel')
>>      expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf")
>>      write.exprs(expr.vals, file= 'Customoutput.csv', sep=",",
>> row.names=F,
>> col.names=T, quote=F)
>>
>> Could you please advise me here on how to modify the script so that I
>> get normalized probe intensities for all the  probe sets?
>>
>> Thank you for your attention and time.
>>
>> Bhargavi
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
Bhargavi Duvvuri M.Sc,
Ph.D
TAS/CAN Postdoctoral Research
Fellow
The Hospital for Sick Children Research Institute
Division of Cell Biology
MARS Centre - Toronto Medical Discovery Tower
101 College street, Rm 12-401 Bay C
Toronto, ON, Canada M5G 1L7
Phone: 416-813-7780
Fax: 416-813-8883
email: bhargavi.duvvuri@sickkids.ca

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