Dear all,

I have a set of microarray data (cDNA) downloaded from GEO, by using
GEOquery, so they are log ratios, and the first 4 probes are shown as:

 ID_REF IDENTIFIER  GSM19  GSM12  GSM18  GSM21  GSM22  GSM20  GSM40  GSM34
GSM14  GSM17  GSM35  GSM36  GSM38  GSM39  GSM41  GSM43  GSM44
1      1     CTNNA1 -0.203 -0.007  0.148  0.025  0.191 -0.048 -0.088 -0.154-
0.135  0.016 -0.061 -0.066 -0.018 -0.201  0.084  0.018 -0.095 -0.228  0.085
2      2       ARF3 -0.080  0.024  0.355 -0.390 -0.151  0.265  0.116 -0.064-
0.492  0.367 -0.271 -0.045  0.194 -0.368 -0.155 -0.069  0.059  0.166 -0.043
3      3       CYC1 -0.195 -0.111 -0.004 -0.979 -0.090  0.151 -0.048 -0.101-
0.040  0.168 -0.034 -0.067 -0.135 -0.103 -0.082  0.118  0.006  0.166  0.032
4      4       UROS -0.080 -0.112 -0.172 -0.080 -0.092  0.020 -0.003  0.089-
0.295 -0.088  0.059 -0.090 -0.007 -0.071 -0.060 -0.195 -0.046 -0.015 -0.117

As you could see, there could be positives and negatives,

Then I tried both affy method (normalize.quantiles) as well as limma method
(normalizeBetweenArrays, with method set to be "quantile")

both of them give the same results:


      GSM19    GSM12     GSM18       GSM21     GSM22     GSM20     GSM40
GSM34      GSM14     GSM17      GSM35     GSM36     GSM38     GSM39
GSM41
1  5.289303 88.37564 136.98926 142.8176316 141.41726  42.40600  15.15747
11.84226  30.113355  84.85460  17.643645 22.238789  87.04374  13.27543
143.75613
2 19.149632 98.97267 189.40666  17.9076053   9.52521 149.97742 101.93708
27.29289  96.930436 184.48253   3.947816 79.184079 160.57487   5.43671
77.20564
3  5.720355 28.42662 104.65321   0.1561842  14.75966 129.44959  22.87303
19.22897   7.171882 138.44284  24.602158 22.053895  26.25147  30.67997
90.81529
4 19.149632 28.11017  21.65734  88.1384325  14.49513  85.97570  61.18536
89.94530  79.579620  21.65732  85.105079 17.353053  92.58163  91.23708
97.58914


It definitely not representing the log ratios here, do any of you know how
could I normalize the original data (in matrix form) so the normalized data
could still present meaningful log ratio result ?

I appreciate for any comment or suggestion

Thanks a lot,

Alex -



-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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