[BioC] Some Genefilter questions

Amy Mikhail a.mikhail at abdn.ac.uk
Mon Dec 4 20:00:18 CET 2006

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]
 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 Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)
       00-44-1224-273256 (office)

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