[BioC] Agi4x44PreProcess - Filtering Probe Function

[Yong Li]

Dear Bjorn,

I am not 100% sure but it seems the problem lies in the way you call 
function filter.probes. If you want to skip the argument limSAT (as you 
did), you will need to explicitly tell targets=targets.

Trying to use targets="infile.txt" will not work. The function 
filter.probes expects a data frame here, not a string of file name.

Hope this helps,
Yong

BJORN GILL wrote:
> Dear List,
> Can anyone help me with the Agi4x44PreProcess - filtering probe function. I am not sure what I am overlooking. 
> The error message says, "Error in filter.probes(aa, control = TRUE, wellaboveBG = TRUE, isfound = TRUE,  :   'targets' is missing". Does this mean, my data files do not have the filtering parameters or it does not recognize the files. 
> If I specify the file name, then it is not recognizing a mandatory column eventhough it is specified in the file."Error in filter.control(ddNORM, ManuelaGO, targets, annotation.package) :   'targets' needs 'GErep' field"
> I have pasted the session info for reference.
> Thank you very much in advance. Bjorn
> Here is the session info.
>>  library("Agi4x44PreProcess")> targets=read.targets(infile="infile.txt") Target File        		FileName Treatment GErepconta 	conta.txt   control     1contb 	contb.txt   control     1contc 	contc.txt   control     1contd 	contd.txt   control     1tumora  	tumora.txt       tumor     2tumorb   	tumorb.txt       tumor     2tumorc   	tumorc.txt       tumor     2tumord  	tumord.txt       tumor     2 >  aa=read.AgilentFE(targets, makePLOT=FALSE)Read conta.txt Read contb.txt Read contc.txt Read contd.txt Read tumora.txt Read tumorb.txt Read tumorc.txt Read tumord.txt    RGList: 	dd$R:	'gProcessedSignal'  	dd$G:	'gMeanSignal'  	dd$Rb:	'gBGMedianSignal'  	dd$Gb:	'gBGUsed'   > aaFILT = filter.probes(aa, 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 = TR
U!
>  E, targets)FILTERING PROBES BY FLAGS 
> Error in filter.probes(aa, control = TRUE, wellaboveBG = TRUE, isfound = TRUE,  :   'targets' is missing > aaFILT = filter.probes(aa, 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="infile.txt")FILTERING PROBES BY FLAGS 
> Error in filter.control(ddNORM, ManuelaGO, targets, annotation.package) :   'targets' needs 'GErep' field
> Bjorn GillPh.D. Candidate in BiologyUniversity of WaterlooOntario, Canada
>  		 	   		  
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