Dear group, I am trying to process some affymetrix CEL files to a format that my programs can understand. For that I need to let my program know the intensity readings(mean and stdv) by name of probe set instead of X,Y coordinates. Using R, can I get a file that will have an extra column of probe set IDs in addition to spot coordinates. Is there a method(steps of commands) to get a file with all spots along with affy probeset. Can I get a output that has an extra column like the following: [INTENSITY] NumberCells=409600 CellHeader=X Y MEAN STDV NPIXELS 1000_at 0 0 384.0 37.3 25 1001_at 1 0 11930.3 907.7 20 Also, is this spot coordinates 0, 0 is always fixed for a prticular chip (Logically speaking it should not change). however, I would like to know more information about this. Thank you. Srini Iyyer

Dear group, I am new to microarrays and bioinformatics field and I am reposting my queries anticipating that some one might help me. Please excuse me. I am trying to process some affymetrix CEL files to a format that my programs can understand. For that I need to let my program know the intensity readings(mean and stdv) by name of probe set instead of X,Y coordinates. Using R, can I get a file that will have an extra column of probe set IDs in addition to spot coordinates. Is there a method(steps of commands) to get a file with all spots along with affy probeset. Can I get a output that has an extra column like the following: [INTENSITY] NumberCells=409600 CellHeader=X Y MEAN STDV NPIXELS 1000_at 0 0 384.0 37.3 25 1001_at 1 0 11930.3 907.7 20 Also, is this spot coordinates 0, 0 is always fixed for a prticular chip (Logically speaking it should not change). however, I would like to know more information about this. Thank you. Srini Iyyer