[BioC] Agi4x44PreProcess
Francois Pepin
fpepin at cs.mcgill.ca
Thu Dec 10 01:50:25 CET 2009
Hi Neel,
you want to have "targets=targets)" at the end of your call to
filter.probes. Otherwise it thinks that targets is the value for for the
limSAT argument.
If you're not going to follow the order of arguments, you should make
sure to name every argument in the function.
Francois
On 12/09/2009 06:56 PM, Neel Aluru wrote:
> Hello,
>
> Can anyone help me in troubleshooting the function for filtering probes. Below is the session info and I am just trying the functions in the user guide.
> Thank you,
>
> Neel
>
> Session info.
>
>> setwd("/Users/Neel/agilent")
>> library("Agi4x44PreProcess")
>> targets=read.targets(infile="infile.txt")
>
> Target File
> X FileName Treatment GErep
> conta cont1 conta.txt control 1
> contb cont2 contb.txt control 2
> contc cont3 contc.txt control 3
> contd cont4 contd.txt control 4
> pcba pcb1 pcba.txt pcb 1
> pcbb pcb2 pcbb.txt pcb 2
> pcbc pcb3 pcbc.txt pcb 3
> pcbd pcb4 pcbd.txt pcb 4
>
>> aa=read.AgilentFE(targets, makePLOT=FALSE)
> Read conta.txt
> Read contb.txt
> Read contc.txt
> Read contd.txt
> Read pcba.txt
> Read pcbb.txt
> Read pcbc.txt
> Read pcbd.txt
>
> RGList:
> dd$R: 'gProcessedSignal'
> dd$G: 'gMeanSignal'
> dd$Rb: 'gBGMedianSignal'
> dd$Gb: 'gBGUsed'
>
>> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
> BACKGROUND CORRECTION AND NORMALIZATION
>
> foreground: MeanSignal
> background: BGMedianSignal
>
> BGmethod: half
> NORMmethod: quantile
> OUTPUT in log-2 scale
>
> ------------------------------------------------------
>> aaFILT = filter.probes(aaNORM, control = TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG= TRUE, sat=TRUE, PopnOL = TRUE, NonUnifOL = TRUE, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = F, annotation.package = "org.Dr.eg.db", flag.counts = TRUE, targets)
> FILTERING PROBES BY FLAGS
>
> Error in filter.probes(aaNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE, :
> 'targets' is missing
>
>
> Neel Aluru
> Postdoctoral Scholar
> Biology Department
> Woods Hole Oceanographic Institution
> Woods Hole, MA 02543
> USA
> 508-289-3607
>
>
>
>
> [[alternative HTML version deleted]]
>
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