Hello All,

I am working on TCGA lung cancer data , I want to compare Average expression of a set of gene (my interested set of gene) in normal and tumor samples. I am wondering that the average expression of these gene in  normal and tumor samples are very simialr in  normalized log2 data , Fig1, (LUAD.uncv2.mRNAseq_RSEM_normalized_log2.txt), but it is different in normalized Z_score data, Fig2,  (LUAD.uncv2.mRNAseq_RSEM_Z_Score.txt).

Fig 1, when using (LUAD.uncv2.mRNAseq_RSEM_normalized_log2.txt) data

![Fig 1][1]


Fig 2, when using (LUAD.uncv2.mRNAseq_RSEM_Z_Score.txt) data
![Fig2][2]

PS: x-axis, same order of genes

So, please help me, which input data should be approprite for this type of comparision.

Thank you...
  [1]: http://s33.postimg.org/9pc7pa9q7/image.png
  [2]: http://s33.postimg.org/3qccl35q7/image.png
Here, Z_Score means:  

    Z_Score = (expression in single tumor sample) - (mean expression in all tumor samples ) / (standard deviation of expression in all tumor samples)

That's why the Z-score for cancer group is very small in your Figure 2. 

And I think for the calculation of Z score for normal samle is something like this way:

    Z_Score = (expression in single normal sample) - (mean expression in all normal samples ) / (standard deviation of expression in all normal samples)

That means this curve only show the fluctuation of the gene expression in that group 

I am pretty sure that you should use the data in Figure 1. 
