Hi I'm attempting to use the spotSegmentation package and I've run the demo using the dataset provided with the package with no problems. However its not clear how to use your own images which I'm presuming will be tiff images for each channel ? Also after you have used the spotseg function you can summarize the data and receive foreground & background (median & mean) for each channel. I'm presuming you extract the background from the foreground for which ever you feel appropriate ? and then use this data from subsequent analysis ? I'd like to also know what the most appropriate way of dealing with NA's is (presumable the "non-found" spots) where the spots in question are printed in duplicate on the array and only one of which is "found". I'm using limma for analysis of data, so I presume I can easily convert this data into MA objects ? Many thanks Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

Hi I'm attempting to use the spotSegmentation package and I've run the demo using the dataset provided with the package with no problems. However its not clear how to use your own images which I'm presuming will be tiff images for each channel ? Also after you have used the spotseg function you can summarize the data and receive foreground & background (median & mean) for each channel. I'm presuming you extract the background from the foreground for which ever you feel appropriate ? and then use this data from subsequent analysis ? I'd like to also know what the most appropriate way of dealing with NA's is (presumable the "non-found" spots) where the spots in question are printed in duplicate on the array and only one of which is "found". I'm using limma for analysis of data, so I presume I can easily convert this data into MA objects ? Many thanks Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919