[BioC] Agi4x44PreProcess

[Francois Pepin]

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
>
>
>
>
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>
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