[BioC] Some Genefilter questions

[Amy Mikhail]

Hi Jenny,

Thanks - just realised my mistake; I forgot that I was just trying to
create the character vector and the next bit was already in your code...

Cheers,
Amy

---------------------------------------------------------------------------
Amy
> 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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>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives:
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-------------------------------------------
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)