[BioC] Agilent zebrafish4x44 database

[Neel Aluru]

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
>> 
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> 

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