[BioC] justRMA?
James W. MacDonald
jmacdon at uw.edu
Tue Dec 11 18:44:10 CET 2012
Hi Bhargavi,
Please don't take things off-list.
On 12/11/2012 12:05 PM, Bhargavi Duvvuri wrote:
> Hello James,
>
> Thank you for your reply.
>
> Here is the new issue I get with RMA:
>
> When I run on Windows operating system I get 34901 probe intensities
> with one or many CEL files. Same output with justRMA, as you said.
>
> However, when I run same on Mac OS and Linux, I would get 23068 probe
> intensities with one or many CEL files. Same output with justRMA.
>
> Same version of R and affy on three operating systems.
What is your output from sessionInfo() on Linux? Make sure you have
loaded the primeviewhsrefseqcdf package first.
Also, what do you get from
length(ls(primeviewhsrefseqcdf))
on Linux?
Best,
Jim
>
> Why would this happen? I can run batch of CEL files only on Mac or
> Linux due to memory issues.
>
> Could you please advise?
>
> Thank you
>
> Bhargavi
>
>
>
> On Mon, Dec 10, 2012 at 9:26 AM, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>> wrote:
>
> 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> <mailto: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 <tel:416-813-7780>
> Fax: 416-813-8883 <tel:416-813-8883>
> email: bhargavi.duvvuri at sickkids.ca
> <mailto:bhargavi.duvvuri at sickkids.ca>
> <mailto: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
>
>
>
>
> --
> 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
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