[BioC] CDF files

[Laurent Gautier]

S Peri wrote:
> Hi, 
>  I am also trying to parse CDF files to get the
> coordinates of the porbesets and their names. The
> reason I need to get is that, I want a reference for
> each probeset on the chip in this case postion on the
> chip. This allows my to query specifically some
> probesets depending on the position.  I know this
> might sound too much, however, I am interested in
> implementing this in the db schema I have.  
> 
> I tried Laurent's suggestions. It worked for one
> probeset.

By induction, it should then work for all probesets.
(and since apparently you want to store everything in a database,
I do not see the problem...)

> Is there any command where I get an object
> with all probesetIDs and their coordinates written
> adjascent to probeset coordinats. 

Follow the second suggestion and make an instance of class Cdf (see 
package 'makecdfenv').

Then:

i <- seq(along=c(mycdf at names))
cbind(mycdf at names.levels[mycdf at names], indices2xy(i, nr=nrow(mycdf at names))
## ...this is untested... you may still have to read the
## documentation...


> Thanks.
> Peri.
> 
> 
> --- Laurent Gautier <lgautier at altern.org> wrote:
> 
> 
>>Srinivas Iyyer wrote:
>>
>>>Hi, 
>>>
>>>CellHeader=X	Y	MEAN	STDV	NPIXELS
>>>  0	  0	152.0	30.0	 25
>>>  1	  0	5024.5	475.3	 20
>>>  2	  0	151.0	25.0	 25
>>>  3	  0	5017.0	558.9	 25
>>>  4	  0	205.5	71.5	 20
>>>
>>>
>>>
>>>
>>>
>>>How can I get to know what 0 0 , 1 0, 2 0
>>
>>correspond
>>
>>>to 1001_at or XXXX_at.  Can some one please help.
>>
>>I
>>
>>>want to get the spot and the corresponding probe. 
>>
>>The information is contained in the relevant CDF
>>file.
>>
>>Did you consider using the 'affy' package ?
>>
>>The help page for the function 'xy2indices' might be
>>worth a look.
>>
>>However, if you want to go from XY coordinates to
>>probe set names often 
>>in your code, the most efficient
>>would be to use the class Cdf (now found in the
>>package 'makecdfenv').
>>
>>
>>L.
>>
>>
>>
>>>Thank you.
>>>
>>>Srini
>>>
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>>
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> 
> 
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