Consider the oligo stack. > dir()[c(63,65,67)] [1] "TisMix_mix8_03_v1_WTGene1.CEL" "TisMix_mix9_01_v1_WTGene1.CEL" [3] "TisMix_mix9_02_v1_WTGene1.CEL" > xo = oligo::read.celfiles(filenames=dir()[c(63,65,67)]) Platform design info loaded. > xa = affy::ReadAffy(filenames=dir()[c(63,65,67)]) > dim(exprs(xo)) [1] 1102500 3 > dim(exprs(xa)) [1] 1102500 3 > rxo = rma(xo) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "probeNames", for signature "GeneFeatureSet" > rxo = oligo::rma(xo) Background correcting... OK Normalizing... OK Summarizing... OK > rxa = affy::rma(xa) Background correcting Normalizing Calculating Expression > dim(exprs(rxo)) [1] 33297 3 > dim(exprs(rxa)) [1] 32321 3 > sessionInfo() R version 2.13.0 Under development (unstable) (2011-03-01 r54628) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hugene10stv1cdf_2.7.1 affyio_1.19.2 [3] affy_1.29.1 pd.hugene.1.0.st.v1_3.0.2 [5] RSQLite_0.9-4 DBI_0.2-5 [7] ff_2.2-1 bit_1.1-6 [9] oligo_1.15.1 oligoClasses_1.13.8 [11] Biobase_2.11.9 loaded via a namespace (and not attached): [1] AnnotationDbi_1.13.13 Biostrings_2.19.11 IRanges_1.9.25 [4] affxparser_1.23.0 preprocessCore_1.13.3 splines_2.13.0 2011/3/3 Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca="">: > Dear Mark, > > Thank you for your answer. > > Please correct me if I'm getting the wrong impression, but doesn't this mean > that just.rma() and rma() are simply wrong in this case? ?And if that's the case > then should they be used for ST data? ?In previous versions of Biocionductor they > simply did not work (there was no cdf environment) but now that they do users will > be using them, generating results that are not complete... > > Best, > Micha? > > > > Mark Cowley <m.cowley at="" garvan.org.au=""> wrote: >> Michal, >> in just.rma and rma, it was assumed that each probe could be in at most 1 >> probeset. once a probe was used, it cannot be reused. >> on the ST arrays, some probes can be in many probesets... so if you use rma, >> eventually, all the probes in a probeset have been used once by the time the >> current probeset needs it & you get NA's. > >> Mark > >> On 24/02/2011, at 8:40 AM, Michal Blazejczyk wrote: > >>> Dear Christian, >>> >>> I am aware of the existence of xps. ?However, we can't use it for our purposes, >>> largely because it is too complicated to set up (or at least, that was the case >>> the last time we looked at it). ?I would still like to know what's happening in >>> just.rma() ?:) >>> >>> Best, >>> Micha? >>> >>> >>> >>> cstrato <cstrato at="" aon.at=""> wrote: >>>> Dear Michal, >>> >>>> As an alternative to just.rma() you could use the Bioconductor package >>>> xps which uses the Affymetrix PGF-file as well as the Affymetrix >>>> annotations, and thus should contain all probesets. xps has also a >>>> vignette, "APTvsXPS.pdf" which compares the results for RMA obtained >>>> from APT vs xps, respectively, for the HuGene 1.0 ST array. >>> >>>> Best regards >>>> Christian >>>> _._._._._._._._._._._._._._._._._._ >>>> C.h.r.i.s.t.i.a.n ? S.t.r.a.t.o.w.a >>>> V.i.e.n.n.a ? ? ? ? ? A.u.s.t.r.i.a >>>> e.m.a.i.l: ? ? ? ?cstrato at aon.at >>>> _._._._._._._._._._._._._._._._._._ >>> >>> >>>> On 2/23/11 7:06 PM, Michal Blazejczyk wrote: >>>>> Dear group, >>>>> >>>>> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level >>>>> probesets that RMA in APT for the Human Gene 1.0 ST array. ?To be specific, 819 probesets >>>>> are missing, and most of them seem to be "real", i.e. they are annotated when I run them >>>>> through NetAffx. >>>>> >>>>> I would like to know why this is happening, and whether it is to be expected or maybe >>>>> it is a bug. >>>>> >>>>> Best regards, >>>>> >>>>> Micha? B?a?ejczyk >>>>> FlexArray Lead Developer >>>>> McGill University and Genome Quebec Innovation Centre >>>>> http://www.gqinnovationcenter.com/services/bioinformatics/flexar ray/index.aspx?l=e >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Michal, yes, I think it's wrong to use rma/just.rma on ST data -- since working this out, I never do (except for using existing array QC pipelines which rely on 'rma' where i don't care about a few missing/erroneous probesets). Thus consider these excellent alternatives: oligo, XPS, or affymetrix- probeset-summarize. I currently use oligo because I can write pure R code with no dependencies on ROOT, but I will probably switch to XPS, because once its installed, the same pipeline can handle ST arrays and older genome arrays & can calculate DABG calls on the ST arrays my 2 cents Mark On 04/03/2011, at 2:24 AM, Michal Blazejczyk wrote: > Dear Mark, > > Thank you for your answer. > > Please correct me if I'm getting the wrong impression, but doesn't this mean > that just.rma() and rma() are simply wrong in this case? And if that's the case > then should they be used for ST data? In previous versions of Biocionductor they > simply did not work (there was no cdf environment) but now that they do users will > be using them, generating results that are not complete... > > Best, > Micha? > > > > Mark Cowley <m.cowley at="" garvan.org.au=""> wrote: >> Michal, >> in just.rma and rma, it was assumed that each probe could be in at most 1 >> probeset. once a probe was used, it cannot be reused. >> on the ST arrays, some probes can be in many probesets... so if you use rma, >> eventually, all the probes in a probeset have been used once by the time the >> current probeset needs it & you get NA's. > >> Mark > >> On 24/02/2011, at 8:40 AM, Michal Blazejczyk wrote: > >>> Dear Christian, >>> >>> I am aware of the existence of xps. However, we can't use it for our purposes, >>> largely because it is too complicated to set up (or at least, that was the case >>> the last time we looked at it). I would still like to know what's happening in >>> just.rma() :) >>> >>> Best, >>> Micha? >>> >>> >>> >>> cstrato <cstrato at="" aon.at=""> wrote: >>>> Dear Michal, >>> >>>> As an alternative to just.rma() you could use the Bioconductor package >>>> xps which uses the Affymetrix PGF-file as well as the Affymetrix >>>> annotations, and thus should contain all probesets. xps has also a >>>> vignette, "APTvsXPS.pdf" which compares the results for RMA obtained >>>> from APT vs xps, respectively, for the HuGene 1.0 ST array. >>> >>>> Best regards >>>> Christian >>>> _._._._._._._._._._._._._._._._._._ >>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >>>> V.i.e.n.n.a A.u.s.t.r.i.a >>>> e.m.a.i.l: cstrato at aon.at >>>> _._._._._._._._._._._._._._._._._._ >>> >>> >>>> On 2/23/11 7:06 PM, Michal Blazejczyk wrote: >>>>> Dear group, >>>>> >>>>> I have noticed that Bioconductor's just.rma() function returns fewer transcript-level >>>>> probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets >>>>> are missing, and most of them seem to be "real", i.e. they are annotated when I run them >>>>> through NetAffx. >>>>> >>>>> I would like to know why this is happening, and whether it is to be expected or maybe >>>>> it is a bug. >>>>> >>>>> Best regards, >>>>> >>>>> Micha? B?a?ejczyk >>>>> FlexArray Lead Developer >>>>> McGill University and Genome Quebec Innovation Centre >>>>> http://www.gqinnovationcenter.com/services/bioinformatics/flexar ray/index.aspx?l=e >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >