Entering edit mode
bzguan@ucdavis.edu
▴
30
@bzguanucdavisedu-5261
Last seen 10.1 years ago
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