[BioC] Agilent zebrafish4x44 database

[Francois Pepin]

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