[BioC] Agilent zebrafish4x44 database

Neel Aluru naluru at whoi.edu
Fri Nov 13 04:35:39 CET 2009 

Thanks, Francois. I am a beginner to R and slowly trying to learn. I appreciate your comments. Now I have pasted the session info. You may be right with regard to ACCNUM mapping. I looked in the zebrafish.db0 package and cannot find the ACCNUMmapping.  I do not understand what you meant by space in "zebrafish.db0".

Thanks once again,

Sincerely, Neel

Following is the session info. 
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
> getwd()
[1] "/Users/Neel"
> setwd("/Users/Neel/agilent")
> getwd()
[1] "/Users/Neel/agilent"
Loading required package: Biobase
Welcome to Bioconductor
  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: limma
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: genefilter
Loading required package: affyPLM
Loading required package: affy

Attaching package: 'affy'
The following object(s) are masked from package:Agi4x44PreProcess :
	 plotDensity 
Loading required package: gcrma
Loading required package: Biostrings
Loading required package: IRanges
Attaching package: 'IRanges'
	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 

Loading required package: preprocessCore
Attaching package: 'affyPLM'
	The following object(s) are masked from package:Agi4x44PreProcess :
	 RLE 
The following object(s) are masked from package:stats :
	 resid,
	 residuals,
	 weights 
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : 
  there is no package called 'beadarray'
Error: package/namespace load failed for 'arrayQualityMetrics'
Loading required package: tcltk
Loading Tcl/Tk interface ... done

limmaGUI can be launched by typing limmaGUI()

Attaching package: 'limmaGUI'
	The following object(s) are masked from package:limma :
	 limmaUsersGuide 
limmaGUI can be launched by typing limmaGUI()
Attaching package: 'limmaGUI'
	The following object(s) are masked from package:limma :
	 limmaUsersGuide 
> 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=TRUE)
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'  

> CV.rep.probes(aa, "zebrafish.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 

Error: getAnnMap: zebrafish.db package not attached and load is FALSE
Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) : 
  error in evaluating the argument 'envir' in selecting a method for function 'mget'

> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = TRUE, makePLOTpost = TRUE)
BACKGROUND CORRECTION AND NORMALIZATION  

	foreground: MeanSignal 
	background: BGMedianSignal 
Hit <Return> to see next plot: 
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	BGmethod:	 half 
	NORMmethod:	 quantile 
	OUTPUT in log-2 scale 

------------------------------------------------------ 
Hit <Return> to see next plot: 
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Hit <Return> to see next plot: 
End of the session


On Nov 12, 2009, at 9:36 PM, Francois Pepin wrote:

> Hi Neel,
> 
> in cases like this, supplying the sessionInfo() is a good idea, as it lets everyone know which versions you are using. As per the posting guide (see the URL at the bottom of this e-mail), having the code snippet initially would also have been helpful.
> 
> I don't have the zebrafish.db0 package installed, so I can't say for sure what the issue is. I don't think you should have the space in "zebrafish.db0 ". It might also be that the zebrafish.db0 package does not have the ACCNUM mapping.
> 
> Now that we've got more information, the others can chime in with more insight.
> 
> Francois
> 
> On 11/12/2009 09:08 PM, Neel Aluru wrote:
>> Hi Francois,
>> 
>> Thanks for your reply. I am trying to calculate the replicated probe coefficient of variation and having trouble understanding it. Here is the syntax I am writing for it.
>> 
>>> CV.rep.probes(aa,"zebrafish.db0 ",foreground ="MeanSignal", raw.data=TRUE, writeR = TRUE, targets)
>> The error message is
>> 
>> Non-CTRL Replicated probes
>> 	foreground:  MeanSignal
>> 		FILTERING BY ControlType FLAG
>> 		RAW DATA: PROBES AFTER ControlType FILTERING:  42990
>> 
>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>>   object 'zebrafish.db0ACCNUM' not found
>> Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) :
>>   error in evaluating the argument 'envir' in selecting a method for function 'mget'
>> 
>> I defined "aa" for reading agilent FE files.
>> 
>> I am not sure if I am doing something wrong. I really appreciate any suggestions how to proceed with it.
>> 
>> Thanks,
>> 
>> Sincerely, Neel
>> 
>> On Nov 12, 2009, at 3:31 PM, Francois Pepin wrote:
>> 
>>> Hi Neel.
>>> 
>>> I'm not sure which database you are talking about here.
>>> 
>>> I haven't used zebrafish arrays, but my experience with human and mouse is that there is very little variation between duplicated probes (ie same sequence and probe id). I would be surprised if zebrafish is any different, as those differences would be purely technical and only depend on the protocol, the reagents used and the person performing the manipulations.
>>> 
>>> Maybe you could clarify if I'm not reading this properly, as I'm confused what a database would have to do with this.
>>> 
>>> Francois
>>> 
>>> On 11/12/2009 03:19 PM, Neel Aluru wrote:
>>>> Hello,
>>>> 
>>>> Does any one has Agilent zebrafish 4x44 database to use for calculating % CV of replicated probes.
>>>> 
>>>> Thank you,
>>>> 
>>>> Neel
>>>> 
>>>> 
>>>> Neel Aluru
>>>> Postdoctoral Scholar
>>>> Biology Department
>>>> Woods Hole Oceanographic Institution
>>>> Woods Hole, MA 02543
>>>> USA
>>>> 508-289-3607
>>>> 
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> 
>> 
>> Neel Aluru
>> Postdoctoral Scholar
>> Biology Department
>> Woods Hole Oceanographic Institution
>> Woods Hole, MA 02543
>> USA
>> 508-289-3607
>> 
>> 
>> 
> 

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

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