Hello James,

Here is the session info after I run justRMA.

R version 2.15.0 (2012-03-30)
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ISBN 3-900051-07-0
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[Previously saved workspace restored]

> library(affy)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

    xtabs

The following object(s) are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
    colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

>    setwd('/home/run/testcel')
>     expr.vals <- justRMA(cdfname = "PrimeViewHsREFSEQcdf")
Loading required package: AnnotationDbi

>     write.exprs(expr.vals, file= 'Customoutput.csv', sep=",",
row.names=F, col.names=T, quote=F)
>
> proc.time()
   user  system elapsed
399.416  21.025 440.413

With length(ls(**primeviewhsrefseqcdf)) I get:

 length(ls(primeviewhsrefseqcdf))
[1] 20367


Thank you

On Tue, Dec 11, 2012 at 12:44 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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@uw.edu<mailto:
>> jmacdon@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@uw.edu <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu
>>
>>         <mailto: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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>> >
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>>
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>>
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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@sickkids.ca
>>         <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca>
>> >
>>         <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca>
>>
>>         <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@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@sickkids.ca <mailto:bhargavi.duvvuri@**
>> sickkids.ca <bhargavi.duvvuri@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@sickkids.ca

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