[BioC] Agi4x44PreProcess

[Neel Aluru]

Dear BioC users,

I have a question regarding filter.probes function in Agi4x44PreProcess. I am analyzing few Agilent 4x44 zebrafish arrays and cannot get function work. I went through the mailing lists for this package as well as AgiMicroRna package. I have seen previously some users have asked questions about filtering probes function. The error message I am getting suggests that some columns are missing in my files. I looked at my files but cannot tell which one is missing as I don't know what this package is looking for. Any help will be highly appreciated. I have pasted the details below.

Thank you

Neel



R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
[R.app GUI 1.34 (5589) x86_64-apple-darwin9.8.0]

> library("Agi4x44PreProcess")
> targets=read.targets(infile="targets2.txt")
 
Target File 
                   FileName Treatment GErep
103-AHRR-a1 103-AHRR-a1.txt     AHRRa     1
103-AHRR-a2 103-AHRR-a2.txt     AHRRa     1
103-AHRR-b1 103-AHRR-b1.txt     AHRRb     2
103-AHRR-b2 103-AHRR-b2.txt     AHRRb     2
102-CONT-1   102-CONT-1.txt      CONT     3
102-CONT-2   102-CONT-2.txt      CONT     3
 
> dd2=read.AgilentFE(targets, makePLOT=FALSE)
Read 103-AHRR-a1.txt 
Read 103-AHRR-a2.txt 
Read 103-AHRR-b1.txt 
Read 103-AHRR-b2.txt 
Read 102-CONT-1.txt 
Read 102-CONT-2.txt 
 
  RGList: 
	dd$R:	'gProcessedSignal'  
	dd$G:	'gMeanSignal'  
	dd$Rb:	'gBGMedianSignal'  
	dd$Gb:	'gBGUsed'  
 
> dim(dd2)
[1] 44407     6
> names(dd2)
[1] "R"       "G"       "Rb"      "Gb"      "targets" "genes"   "other"  
> CV.rep.probes(dd2,"zf.db",foreground="MeanSignal", raw.data=TRUE,writeR=FALSE,targets)

------------------------------------------------------ 
Non-CTRL Replicated probes 
	foreground:  MeanSignal 
		FILTERING BY ControlType FLAG 
		RAW DATA: PROBES AFTER ControlType FILTERING:  42990 

------------------------------------------------------ 
	REPLICATED NonCtrl Probes 21495 
	UNIQUE probes 21495 
	DISTRIBUTION OF REPLICATED NonControl Probes 
reps
    1 
21495 
	# REPLICATED (redundant) probeNames 21495 
------------------------------------------------------ 
MEDIAN % CV 
103-AHRR-a1 103-AHRR-a2 103-AHRR-b1 103-AHRR-b2  102-CONT-1  102-CONT-2 
      2.477       1.279       1.454       2.157       1.689       1.342 
------------------------------------------------------ 
> genes.rpt.agi(dd2,"zf.db",raw.data=TRUE,WRITE.html=FALSE,REPORT=FALSE)

GENE SETS: same genes interrogated by different probes 
		FILTERING BY ControlType FLAG 
		RAW DATA: PROBES AFTER ControlType FILTERING:  42990 

	INPUT DATA: RAW 
	CHIP: zf.db 

	PROBE SETS (NON-CTRL prob rep. x 10):	 21495 
	GEN-SETS (REPLICATED GENES):		 2281 
	PROBES in gen-sets:			 5012 
> ddNORM=BGandNorm(dd2, 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 

------------------------------------------------------ 
> ddFILT=filter.probes(ddNORM, control=TRUE,wellaboveBG=TRUE, isfound=TRUE,wellaboveNEG=TRUE,sat=TRUE,PopnOL=TRUE,NonUnifOL=T, nas=TRUE,limWellAbove=75,limISF=75,limNEG=75,limPopnOL=75,limNonUnifOL=75, limNAS=100,makePLOT=F,annotation.package="zf.db",flag.counts=T, targets=targets)
FILTERING PROBES BY FLAGS 


FILTERING BY ControlType FLAG 
Error in data.frame(PROBE_ID, as.character(probe.chr), as.character(probe.seq),  : 
  arguments imply differing number of rows: 42990, 0




Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607