
Hi,

I have run gcrma function to normalized my dataset through “command line gcrma”, affylmGUI and oneChannelGUI package. I got different result. “commad line gcrma” and affylmGUI gave similar numerical result.  But oneChannelGUI give different result.

Below are example results. The columns are my 8 array. 
The “command line gcrma 
117_at	7.055748003	6.745033354	6.905952402	6.89984871	5.427986926	5.487144022	5.114700923	5.32301841
121_at	6.072564588	6.038053861	6.038053861	6.038053861	6.038053861	6.038053861	6.038053861	6.038053861
1255_g_at	2.184719955	2.184719955	2.184719955	2.184719955	2.184719955	2.184719955	2.184719955	2.184719955
affylmGUI gcrma
117_at	7.050791518	6.740370684	6.901693137	6.89418791	5.423481103	5.482261696	5.110524671	5.31888015
121_at	6.079636466	6.04510978	6.04510978	6.04510978	6.04510978	6.04510978	6.04510978	6.04510978
1255_g_at	2.184730201	2.184730201	2.184730201	2.184730201	2.184730201	2.184730201	2.184730201	2.184730201

oneChannelGUI gcrma result are

117_at	5.132868736	4.705035992	4.894346799	4.986446054	4.072583937	4.087168465	3.926364524	3.967091209
121_at	3.893796881	3.849060442	3.806120005	3.887322359	3.975799975	3.699148114	3.850412448	3.983149921
1255_g_at	2.38946722	2.518604015	2.418365149	2.281908869	2.309105889	2.296133099	2.21029538	2.272567028

Do they suppose to give identical output results as the input datasets are the same?

I want to use other features from oneChannelGUI. But I want to make sure that it gives correct normalized result first.

Thanks for the help

ying


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