Hi,
Q1. What does print(cdf) on that CDF below report? By default you get
an exception if you try to use an ASCII CDF.
Q2. What is your sessionInfo()?
/Henrik
On Fri, Dec 4, 2009 at 2:10 PM, zaid <z...@genomedx.com> wrote:
> Hi Mark,
>
> Actually the run took about 14 hours.
>
> I thought I was using a binary CDF file but it seems the one I used is
> ASCII. (shouldnt the program warn me if Im not uisng binary?)
>
> They are on local disk and we want to do probeset-only. (FYI the
> folder that contains the raw data is 2.33 GB in size).
>
> Now if I try it with binary CDF then it should make all the
> difference?
>
> Thanks again for your help.
>
> Here are the commands used:
>> library(aroma.affymetrix)
>>
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(chipType)
>> print(cdf)
>> csX <- AffymetrixCelSet$byName("tissues", cdf=cdf)
>> print(csX)
>> setCdf(csX,cdf)
>> bc <- RmaBackgroundCorrection(csX)
>> plmTr <- ExonRmaPlm(csX, mergeGroups=TRUE)
>> fit(plmTr, verbose=verbose)
>> qamTr <- QualityAssessmentModel(plmTr)
>> plotNuse(qamTr)
>>
>> plotRle(qamTr)
> ------------------------------
>
> PS. I am using a different techqniue for normalization.
>
> Thanks,
> Zaid
>
> On Dec 4, 12:43 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>> Hi Zaid.
>>
>> As I mentioned before, I'd be careful with fitting models on
>> unnormalized data, but I'll assume you know what you are doing.
>>
>> Definitely no need to run things in smaller chunks. aroma.affymetrix
>> does this already to save on memory. The first time through may take
>> a bit longer, but still, 6.5 hours does seem a bit long for 38 samples.
>>
>> What CDF are you using? Binary or ASCII? Probeset-only or gene-
>> based? Are your files on a local disk, or over a network mount?
>>
>> Cheers,
>> Mark
>>
>> On 4-Dec-09, at 12:25 PM, zaid wrote:
>>
>>
>>
>>
>>
>> > Hello Mark,
>>
>> > Thank you for your help.
>>
>> > I'm running the aroma.affymetrix package in R with no normalization as
>> > you have outlined.
>> > I'm using 38 cel files and running a windows vista 64 bit edition on a
>> > quad core intel core 2 processor with 8 gigs of RAM.
>>
>> > the last two steps of "plmTr <- ExonRmaPlm(csX, mergeGroups=TRUE) #
>> > put in the
>> > AffymetrixCelSet here you want to fit PLM on
>> > fit(plmTr, verbose=verbose) " are taking a long time. So far that
>> > step has been running for about 6 and a half hours (job not done yet).
>>
>> > Is that normal? or do I need to run the cel files in smaller chunks?
>>
>> > Thanks in advance
>>
>> > Zaid
>>
>> > On Nov 30, 1:22 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>> >> Hi Elai/Zaid.
>>
>> >> You'll want to be careful with all this (i.e. linear models on
>> >> unnormalized data ... or maybe you are standardizing some other way),
>> >> but yes you can run the probe level model fits on any
>> >> AffymetrixCelSet
>> >> object.
>>
>> >> The standard RMA procedure would BG adjust, then quantile normalize,
>> >> then fit the PLMs:
>> >> cs <- AffymetrixCelSet$byName("BCGC_2006", cdf=cdf)
>> >> bc <- RmaBackgroundCorrection(cs, tag="coreR2")
>> >> csBC <- process(bc,verbose=verbose)
>> >> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>> >> csN <- process(qn, verbose=verbose)
>> >> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
>> >> fit(plmTr, verbose=verbose)
>>
>> >> You could replace this simply with:
>>
>> >> csX <- AffymetrixCelSet$byName("BCGC_2006", cdf=cdf)
>> >> [...maybe do something else to csX...]
>> >> plmTr <- ExonRmaPlm(csX, mergeGroups=TRUE) # put in the
>> >> AffymetrixCelSet here you want to fit PLM on
>> >> fit(plmTr, verbose=verbose)
>>
>> >> Cheers,
>> >> Mark
>>
>> >> On 30-Nov-09, at 3:32 PM, davic...@gmail.com wrote:
>>
>> >>> Henrik
>> >>> Is it possible to use aroma to run an RMA implementation without
>> >>> quantile normalization? Zaid- have you tried this?
>> >>> Best,
>> >>> Elai
>> >>> CSO
>> >>> GenomeDx Biosciences
>>
>> >>> On Nov 28, 5:51 am, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>> >>>> Hi Zaid,
>>
>> >>>> I think you have mistaken the aroma.affymetrix mailing list as
>> >>>> being a
>> >>>> mailing list for Affymetrix software - this forum is only for
>> >>>> aroma.affymetrix related topics. Please use the appropriate
>> >>>> official
>> >>>> Affymetrix forum for their APT software:
>>
>> >>>> https://www.affymetrix.com/community/forums/index.jspa
>>
>> >>>> That way you also know you will get the correct answer from the
>> >>>> correct source. Your question might even have been answered there
>> >>>> before (I don't know).
>>
>> >>>> /HenrikOn Thu, Nov 26, 2009 at 9:22 PM, zaid <z...@genomedx.com>
>> >>>> wrote:
>> >>>>> I tried running the 64 bit version of the command tool apt. I was
>> >>>>> not
>> >>>>> able to find any information to run the command with no
>> >>>>> normalization.
>>
>> >>>>> I tried many different commands such as: apt-probeset-summarize -a
>> >>>>> rma-
>> >>>>> bg,pm-only,sea
>>
>> >>>>> Any ideas on how I can run that tool with no normlization.
>>
>> >>>>> Thanks
>>
>> >>>>> --
>> >>>>> When reporting problems on aroma.affymetrix, make sure 1) to run
>> >>>>> the latest version of the package, 2) to report the output of
>> >>>>> sessionInfo() and traceback(), and 3) to post a complete code
>> >>>>> example.
>>
>> >>>>> You received this message because you are subscribed to the Google
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>> >>>>> For more options, visit this group
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>>
>> >>> --
>> >>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >>> latest version of the package, 2) to report the output of
>> >>> sessionInfo() and traceback(), and 3) to post a complete code
>> >>> example.
>>
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>>
>> >> ------------------------------
>> >> Mark Robinson, PhD (Melb)
>> >> Epigenetics Laboratory, Garvan
>> >> Bioinformatics Division, WEHI
>> >> e: m.robin...@garvan.org.au
>> >> e: mrobin...@wehi.edu.au
>> >> p: +61 (0)3 9345 2628
>> >> f: +61 (0)3 9347 0852
>> >> ------------------------------- Hide quoted text -
>>
>> >> - Show quoted text -
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest version of the package, 2) to report the output of
>> > sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>> > You received this message because you are subscribed to the Google
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>>
>> ------------------------------
>> Mark Robinson, PhD (Melb)
>> Epigenetics Laboratory, Garvan
>> Bioinformatics Division, WEHI
>> e: m.robin...@garvan.org.au
>> e: mrobin...@wehi.edu.au
>> p: +61 (0)3 9345 2628
>> f: +61 (0)3 9347 0852
>> ------------------------------- Hide quoted text -
>>
>> - Show quoted text -
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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