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 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. Thanks in advance. JS.