[BioC] Some Genefilter questions

[Jenny Drnevich]

Oops - forgot to mention in my last post that the only way I've been able 
to remove probesets from AffyBatch objects was to use Ariel's 
'RemoveProbes' function that was referenced previously in this thread.

Jenny

At 01:21 PM 12/4/2006, Jenny Drnevich wrote:
>Hi Amy,
>
>You've got two different problems here. 1) You can't subset an AffyBatch
>with probeset names because it contains individual probe values. Actually,
>I don't think you can subset an AffyBatch row-wise at all, period.
>
>2) You can subset an exprSet or ExpressionSet object row-wise using
>probeset names, but not like you're trying to do. You can't use "-" with a
>character vector to remove those probesets, but you can use a character
>vector to keep probesets. There are several ways to do this - here's one:
>
>new.eset <- eset[setdiff(geneNames(Baseage.rawdata), parasites) , ]
>
>Cheers,
>Jenny
>
>At 01:00 PM 12/4/2006, Amy Mikhail wrote:
> >Hi all,
> >
> >Sorry to bring this interesting discussion back to the mundane again for a
> >minute, but when trying to create the "parasites" character vector from my
> >affybatch object, removing the parasite probe sets with Robert's suggested
> >code is giving me an error:
> >
> >
> > > parasites <- grep("^Pf", geneNames(Baseage.rawdata), value=TRUE)
> > > parasites
> >[2965] "Pf.4.138.0_CDS_at"      "Pf.4.139.0_CDS_at"
> >[2967] "Pf.4.14.0_CDS_at"       "Pf.4.140.0_CDS_at"
> >[2969] "Pf.4.142.0_CDS_at"      "Pf.4.144.0_CDS_at"
> >[2971] "Pf.4.146.0_CDS_at"      "Pf.4.147.0_CDS_at"
> >[2973] "Pf.4.148.0_CDS_at"      "Pf.4.149.0_CDS_at"   ###etc###
> >
> > > Mossie.rawsub = Baseage.rawdata[-parasites,]
> >Error in -parasites : invalid argument to unary operator
> >In addition: Warning message:
> >The use of abatch[i,] and abatch[i] is decrepit. Please us abatch[,i]
> >instead.
> >  in: Baseage.rawdata[-parasites, ]
> >
> >
> >If I try as the warning message suggests, I get another error:
> >
> > > Mossie.rawsub <- Baseage.rawdata[-,parasites]
> >Error: syntax error in "Mossie.rawsub <- Baseage.rawdata[-,"
> >
> >Or variations on a theme...
> >
> > > Mossie.rawsub <- Baseage.rawdata[,-parasites]
> >Error in -parasites : invalid argument to unary operator
> >
> >
> >I could not find the first error in the bioconductor archives.
> >
> >Any ideas?
> >
> >Many thanks,
> >Amy
> >
> >
> >
> >-------------------------------------------
> >Amy Mikhail
> >Research student
> >University of Aberdeen
> >Zoology Building
> >Tillydrone Avenue
> >Aberdeen AB24 2TZ
> >Scotland
> >Email: a.mikhail at abdn.ac.uk
> >Phone: 00-44-1224-272880 (lab)
> >        00-44-1224-273256 (office)
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu
>
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