[BioC] justRMA?

[James W. MacDonald]

Hi Bhargavi,

On 12/9/2012 1:38 AM, Bhargavi Duvvuri wrote:
> 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?

It shouldn't. I don't have 350 of the same type of celfile to test this 
with, so I would suggest trying a subset (like 100) and see how that 
goes. You might be getting an error that you didn't notice.

Best,

Jim


>
> Please advise.
>
> Thank you
>
> Bhargavi
>
> On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at 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 at sickkids.ca <mailto:bhargavi.duvvuri at sickkids.ca>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099