[BioC] affy cel + cdf files content

[Robert Gentleman]

On Mon, Jul 01, 2002 at 02:39:31PM +0200, Laurent Gautier wrote:
> On Fri, Jun 28, 2002 at 08:23:07AM +0200, julien.sylvestre@wotan.ens.fr wrote:
> > This message is not directly related to Bioconductor yet I hope it might be of general interest for users...
> > 
> > The first line of an Affymetrix Yg_s98 yeast chip .cel file looks like this
> > X	Y	MEAN	STDV	NPIXELS
> > 0	0	232	45	36
> > I read about 100 pixels were used whereas it seems that no more than 36 are used here. 
> > How is the svd calculated ?
> 

  The mean is actually the 75th percentile. I believe that the STDV is 
 actually the standard deviation (as defined in any stats book). Both
 are based on the pixels used as I recall. But in all cases, one
 really has to refer to Affymetrix documentation. This is generally
 supplied when you buy chips and or a machine. Some of it is available
 on their website www.affymetrix.com.

   Robert
> 
> The answer lies probably somewhere in the documentation provided by the manufacturer of the chips... (sorry do not have it with me at the moment)...
> A mix a of recollection and guess would make me say that this the the svd of
> the signal for the pixels consituting a 'spot'.
> 
> 
> > 
> > The first line of the corresponding .cdf file reads : 
> > X	Y	PROBE	PLEN	ATOM	INDEX	MATCH	BG
> > 167	80	N	20	1	42887	0	0
> > Can anyone tell me the meaning of the last 6 columns.
> > 
> 
> 
> The Cdf files are more complex things. If interest in the gory details, you
> can read the C code. I wrote something about their structure a long time
> ago but never found the time to put it anywhere... (and now I do not even
> remember where I put it... ;) ).
> 
> >From the top of my head, PROBE says whether it's a true probe or not, PLEN gives
> it length in bases, atom relates to PPSet (try 'class?Cdf' to know more), INDEX
> is like a unique ID for the probe, MATCH and BG I do not remember (sorry busy-busy).
> 
> 
> 
> Hopin' it helps,
> 
> 
> 
> Laurent
> 
> 
> 
> 
> > Thanks in advance.
> > 
> > JS.
> > 
> > 
> > 
> > 
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> 
> -- 
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
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