[BioC] Agilent zebrafish4x44 database
Neel Aluru
naluru at whoi.edu
Fri Nov 13 03:08:59 CET 2009
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
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