[BioC] scan date information
rob.dunne at csiro.au
Tue Sep 22 00:42:22 CEST 2009
Thanks for that.
I am not using the development version yet but I will look out for the
Saroj, your method doesn't work for me, perhaps your cel file is ascii?
strings SB_20D.CEL | grep DatHeader
However, I have found
$ grep --text d.a.t.e. SB_20D.CEL
the "--text" option makes grep read a binary file as thought it was
text. I am not sure why I need the dots in date.
Patrick Aboyoun wrote:
> 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.
> 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?
>> 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
>>> does not pick up the date.
>>> Unfortunately in many experiments the scan date turns out to be the
>>> major effect.
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