Biopolymeric array scanners capable of automatic scale factor selection for a plurality of different dyes, and methods for making and using the same

Abstract

Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same. The subject invention finds use in a variety of different applications, including both genomics and proteomics applications.

1 - 9 . (canceled) 
   
   
       10 . A collection of nominal scale factors for a plurality of three or more dyes recorded onto a computer readable medium. 
   
   
       11 . The collection according to  claim 10 , wherein said collection further comprises first order crosstalk for each member of said plurality. 
   
   
       12 . A biopolymer array multi channel optical detector comprising a collection of nominal scale factors according to  claim 10  recorded on a computer readable medium thereof. 
   
   
       13 . The detector according to  claim 12 , wherein said optical detector is an optical scanner. 
   
   
       14 . The biopolymer array optical detector according to  claim 12 , wherein said collection further comprises first order crosstalk data for each member of said plurality. 
   
   
       15 - 18 . (canceled) 
   
   
       19 . A method of reading a biopolymeric array with a biopolymeric array scanner, said method comprising:
 (a) inputting at least one dye selection into said biopolymeric array scanner so that said scanner automatically selects a dye specific scale factor for reading said array; and   (b) reading said array with said biopolymer array scanner to obtain a result, wherein said reading comprises using said automatically selected dye specific scale factor.   
   
   
       20 . The method according to  claim 19 , wherein said scanner automatically selects a dye specific scale factor by employing a collection of nominal scale factors according to  claim 10 . 
   
   
       21 . The method according to  claim 20 , wherein said dye specific scale factor is automatically set by adjusting scanner instrument gain based on a nominal scale factor. 
   
   
       22 . The method according to  claim 20 , wherein said dye specific scale factor is equal to a master scale factor. 
   
   
       23 . The method according to  claim 19 , wherein said inputting is by reading a barcode on said array, wherein said barcode includes said dye selection. 
   
   
       24 . The method according to  claim 19 , wherein said method further comprises making a first order correction for crosstalk. 
   
   
       25 . The method according to  claim 24 , wherein said correction comprises reducing said crosstalk. 
   
   
       26 . The method according to  claim 25 , wherein said crosstalk is reduced by reducing excitation power of said scanner. 
   
   
       27 . The method according to  claim 25 , wherein said crosstalk is reduced by employing a filter. 
   
   
       28 . The method according to  claim 24 , wherein said method comprises reducing pixel saturation arising from crosstalk. 
   
   
       29 . The method according to  claim 24 , wherein said method comprises increasing signal to noise ratio. 
   
   
       30 . The method according to  claim 24 , wherein said scanner employed in said method is a scanner according to  claim 12  and said collection further comprises first order crosstalk data for each member of said plurality. 
   
   
       31 . The method according to  claim 19 , wherein said biopolymer array is chosen from a polypeptide array and a nucleic acid array. 
   
   
       32 . A method comprising transmitting a result from reading a biopolymeric array according to a method of  claim 19 , from a first location to a second location. 
   
   
       33 . The method of  claim 32 , where said second location is a remote location. 
   
   
       34 . A method comprising receiving data representing said result of a scan obtained by the method of  claim 19 . 
   
   
       35 . A kit for use in a biopolymer array optical scanner, said kit comprising:
 (a) a computer-readable medium according to  claim 10 ; and   (b) instructions for operating said scanner according to said programming.   
   
   
       36 . The kit according to  claims 30 , wherein the kit further includes instructions for installing the encoded instructions. 
   
   
       37 . A method of reading a biopolymeric array with a biopolymeric array scanner that includes at least a first and second detection channel, said method comprising:
 (a) inputting at least one dye selection into said biopolymeric array scanner so that said scanner reduces the possibility of pixel saturation arising from any crosstalk of said dye from said first into said second detection channel; and   (b) reading said array in at least a first and second detection channel with a biopolymer array scanner to obtain a result,   
   
   
       38 . The method according to  claim 37 , wherein said possibility of pixel saturation is reduced by reducing detector gain in said second channel. 
   
   
       39 . A method of reading a biopolymeric array with a biopolymeric array scanner that includes at least a first and second detection channel, said method comprising:
 (a) inputting at least one dye selection into said biopolymeric array scanner so that said scanner identifies the possibility of pixel saturation arising from any crosstalk of said dye from said first into said second detection channel;   (b) reading said array in at least a first and second detection channel with a biopolymer array scanner to obtain a result; and   (c) if the possibility of crosstalk is present, rereading said array in at least said first and second detection channels wherein sensitivity in at least one of said detection channels is modulated.   
   
   
       40 . A method of reading a biopolymeric array with a biopolymeric array scanner that includes at least a first and second detection channel, said method comprising:
 (a) inputting at least one dye selection into said biopolymeric array scanner so that said scanner identifies the possibility of pixel saturation arising from any crosstalk of said dye from said first into said second detection channel;   (b) reading said array in at least a first and second detection channel with a biopolymer array scanner to obtain a result; and   (c) if the possibility of crosstalk is present, flagging saturated features as arising because of said crosstalk.