[BioC] Quality Control of Exon arrays using xps?

[cstrato]

Dear Achilleas,

I must admit that it is not quite clear to me what you want to do.

What do you mean with BGP file? Do you mean the Affymetrix "*.bgp" file? 
This file is not necessary since it contains redundant information 
already present in the "*.pgf" file.

What do you mean with bgrd_mean and pm_mean?

The mask for genomic bgrd is -1 (32768) and for antigenomic bgrd -2 
(65536).
Using "export.scheme()" you can extract the information from the 
different scheme trees, see "?validTreetype", e.g. the "*.scm" tree 
contains the (x,y) coordinates and mask for the UNIT_ID and PROBESET_ID.

I am not sure if this answers your question.

Best regards
Christian


On 12/22/10 9:32 PM, Achilleas Pitsillides wrote:
> Dear Christian,
> Thanks for the prompt response and at the same time I apologize  for my so
> late acknowledgement. One of the things that I am trying to do is check the
> some of the following pm_mean and bgrd_mean evaluated from the probes listed
> in the BGP file. I am just learning my way around the xps package but it
> seems that the BGP file information is not in the schemeTreeSet. In addition
> some times I need to view specific control probes and the way I go about
> that feels  rather clunky (that's were my previous question about the
> description of the exonmask came in. For example to select the probes
> related to the polya_splike. I obtain the annotation frame find the UNIT_IDs
> that correspond to the polya_spike genename and then use the Mask info to
> get the corresponding X Y co-ordinates of the raw intensity values and then
> unravel those with something of the form Y*2560+X+1 to get the position in
> the intensity file. Is there a more direct way to do this?
>
> Thanks in advance,
> Achilleas
>
> On Mon, Dec 20, 2010 at 12:34 PM, cstrato<cstrato at aon.at>  wrote:
>
>> Dear Achilleas,
>>
>> It depends what you are looking for. Currently xps supports hist() (or
>> root.density()), boxplot (or root.profile()), nuseplot(), rleplot().
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>>
>>
>> On 12/20/10 5:44 PM, Achilleas Pitsillides wrote:
>>
>>> Hi all,
>>> I was was wondering what if there is an easy way to do evaluate QC
>>> (quality
>>> control) on exon arrays.
>>> For Gene arrays I used simpleAffy but that works only on an affybatch
>>> object.
>>>
>>> Thanks in advance,
>>> Achilleas
>>>
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>>>
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