[BioC] Agilent zebrafish4x44 database

Francois Pepin fpepin at cs.mcgill.ca
Fri Nov 13 04:52:35 CET 2009 

Your original code had CV.rep.probes(aa,"zebrafish.db0 ",...

I'm assuming this was just a typo in recopying the code, as it wouldn't 
work if you had the space after the 0.

By sessionInfo(), I meant the output of the sessionInfo() function.

What you just posted is different than before. You have an error loading 
beadarray and you haven't loaded zebrafish.db0, leading to a different 
error than originally. Please try to be consistent, otherwise it's very 
difficult to pinpoint the problem.

As it is, I believe the issue is that Agi4x44PreProcess::CV.rep.probes 
always expects a ACCNUM mapping and none exist in zebrafish.db0. The 
solution here would be to get them to talk to one another properly.

Marc, is there be a recommended way to deal with this? Is there a basic 
mapping that every annotation package should use? Or should a package 
maintainer be aware of all existing variations that exist?

Francois

On 11/12/2009 10:35 PM, Neel Aluru wrote:
> 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:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
>
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
>
> 	BGmethod:	 half
> 	NORMmethod:	 quantile
> 	OUTPUT in log-2 scale
>
> ------------------------------------------------------
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> Hit<Return>  to see next plot:
> 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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