[BioC] scan date information

[Patrick Aboyoun]

Robert,
The answer depends on which version of R and BioC are you using. If you 
are using R <= 2.9, BioC <= 2.4, you will need to devise your own 
method; one of which was given by Saroj. If you are using R-devel and 
BioC 2.5 (devel), the eSet abstract class and its derived classes such 
as ExpressionSet contain a new slot called protocolData that contains an 
AnnotatedDataFrame object. This slot is to be populated by metadata 
contained in microarray data files. In BioC 2.5 (devel) the 
read.affybatch from affy and read.celfile from affyio add a ScanData 
column to the protocolData slot with the metadata you are looking for.


Cheers,
Patrick


Saroj K Mohapatra wrote:
> Hi Rob:
>
> I have a file called _16.CEL. I want to find out the date information 
> in its header. The following gives me:
>
> $ strings _16.CEL | grep DatHeader
> DatHeader=[2..65534]  _16:CLS=7365 RWS=7365 XIN=1  YIN=1  VE=30        
> 2.0 10/27/06 10:57:45 50207590  M10 
> I find a date 10/27/06. Is this what you are looking for?
>
> Best,
>
> Saroj
>
>
> Robert Dunne wrote:
>> Hi List,
>>
>> I apologise for what may be a very simple question. How can I retrieve
>> the scan date information from cel files?
>>
>> I can find the information using some editors, kate under linux shows
>> "a f f y m e t r i x - s c a n - d a t e   ( 2 0 0 8 - 0 4 - 0 3"
>> but I can't find it all all using vi or emacs. I suppose this is 
>> something to do with encoding.
>> Also "string file.cel | grep "d a t e"" does not work.
>>
>> I have tried the affxparser library but
>> readCelHeader("file.cel")
>> does not pick up the date.
>>
>> Unfortunately in many experiments the scan date turns out to be the 
>> major effect.
>>
>> Bye
>> Rob
>>
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