[BioC] justRMA?

[James W. MacDonald]

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