[BioC] affy cel + cdf files content

[Laurent Gautier]

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 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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