[BioC] beadarray package: problem finding Illumina annotation for Human660w_quad bead chip

[bzguan at ucdavis.edu]

Hi,

I have data from Illumina Human660w_quad beadchip.  I use the suggestAnnotation function to 
identify the platform and got zero overlaps with the arrays listed in the suggestAnnotation output.  
What should I use for the illuminaAnnotation option in the readIllumina function?  Below I have 
pasted the result of the suggestAnnotation run.

Thanks for any help,
Anna

> checkPlatform(BLData, verbose = TRUE)
Percentage of overlap with IDs on this array and known expression platforms
HUMANREF8_V3_0_R1_11282963_A_WGDASL        HumanHT12_V3_0_R3_11283641_A        
HumanHT12_V4_0_R1_15002873_B        HumanHT12_V4_0_R2_15002873_B 
                                  0                                   0                                   0                                   0 
HumanHT12_V4_0_R2_15002873_B_WGDASL                        HumanRef8_V1        
HumanRef8_V2_0_R2_11223162_A        HumanRef8_V2_0_R4_11223162_A 
                                  0                                   0                                   0                                   0 
       HumanRef8_V3_0_R0_11282963_A        HumanRef8_V3_0_R3_11282963_A                         
HumanWG6_V1         HumanWG6_V2_0_R2_11223189_A 
                                  0                                   0                                   0                                   0 
        HumanWG6_V2_0_R4_11223189_A              HumanWG6_V2_11223189_B         
HumanWG6_V3_0_R3_11282955_A                        MouseRef8_V1 
                                  0                                   0                                   0                                   0 
       MouseRef8_V1_1_R4_11234312_A        MouseRef8_V2_0_R3_11278551_A                         
MouseWG6_V1         MouseWG6_V1_1_R4_11234304_A 
                                  0                                   0                                   0                                   0 
                      MouseWG6_V1_B         MouseWG6_V2_0_R3_11278593_A         
RatRef12_V1_0_R5_11222119_A 
                                  0                                   0                                   0 
[1] "Humanv3"
Warning messages:
1: 'checkPlatform' is deprecated.
Use 'suggestAnnotation' instead.
See help("Deprecated") and help("beadarray-deprecated"). 
2: In suggestAnnotation(data = BLData, verbose = verbose) :
  Choice of platform may not be accurate. Consider re-running checkPlatform with verbose = TRUE 
option