RG -> MA !!!!!!

Ha~
Just figured it out ~~~~~
The program read in the red/green raw data (intensities), and then convert them to M/A values. So if checking the data before/after normalization, we can find out the variables were changed, from $R & $G to $M & $A. That's why we can not get MA plots by using maQualityPlots, which converts $R/$G to $M/$A. How could we expect it to convert a dataset which is already $M/$A !? Right?

BEFORE normalization

AFTER normalization

>rawdata <- read.GenePix(target=ArrayInfo) >rawdata An object of class "marrayRaw" @maRf 6Hs.195.1.gpr 6Hs.168.gpr 6Hs.166.gpr 6Hs.187.1.gpr 6Hs.194.gpr [1,] 227 370 139 69 187 [2,] 208 273 181 80 213 [3,] 239 288 238 77 377 [4,] 247 301 228 91 329 [5,] 221 290 218 91 351 6Hs.243.1.gpr [1,] 241 [2,] 241 [3,] 307 [4,] 280 [5,] 236 23179 more rows ... @maGf 6Hs.195.1.gpr 6Hs.168.gpr 6Hs.166.gpr 6Hs.187.1.gpr 6Hs.194.gpr [1,] 357 304 189 106 218 [2,] 292 235 255 133 216 [3,] 284 223 256 123 290 [4,] 320 254 302 141 301 [5,] 361 290 328 156 327 6Hs.243.1.gpr [1,] 165 [2,] 183 [3,] 194 [4,] 252 [5,] 247 23179 more rows ... . . .

>NormalizedData=maNorm(rawdata) >NormalizedData An object of class "marrayNorm" @maA 6Hs.195.1.gpr 6Hs.168.gpr 6Hs.166.gpr 6Hs.187.1.gpr 6Hs.194.gpr 6Hs.243.1.gpr [1,] 6.895683 7.298095 NA NA NA 3.336213 [2,] 5.965369 6.322153 5.608070 3.953445 NA 5.213656 [3,] 6.332001 5.879320 6.272724 3.390680 6.759634 5.960176 [4,] 6.765325 6.701772 6.569456 4.761781 6.698837 6.356586 [5,] 6.821026 6.923822 6.699372 5.099223 6.954853 5.620098 23179 more rows ... @maM 6Hs.195.1.gpr 6Hs.168.gpr 6Hs.166.gpr 6Hs.187.1.gpr 6Hs.194.gpr 6Hs.243.1.gpr [1,] -0.4520881 0.11756657 NA NA NA 5.2940001 [2,] -0.1146129 0.02906567 -0.5395663 -0.9326132 NA 1.2865839 [3,] 0.7722506 0.91978728 0.8007346 -0.6557331 0.69575087 2.0297161 [4,] 0.2966088 0.07101715 -0.2995052 -0.2816260 0.01501081 0.3527075 [5,] -0.5549713 -0.56805515 -0.6199517 -0.6012264 -0.21962736 -0.2105729 23179 more rows ... . . .