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. > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent

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. > > > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B28 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

On Mon, Jul 01, 2002 at 09:52:04AM -0400, Robert Gentleman wrote: > 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 > > Thanks for the clear answer Robert. In haste I only generated almost random blurb. I remembered observing lines like below in the header of CEL files --------------- Algorithm=Percentile AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;Outli erLow:1.004 -------------- ...I do not know if there is a way to change the algorithm/parameters in MAS... L.