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Hello,
I am trying to do a microarray analysis on a time-series (5 time points) gene expression (GE) data of 3000 genes. I want to calculate all Vs all (3000 Vs 3000 genes') Pearson correlation coefficient (PCC) values. I searched a lot in literature and found that studies use values that are 'Log (base 2) of the ratio of the median of test spot's intensity to median of control's intensity'.
The intensity values are already normalised (background normalised). Whereas, some studies subtract the control GE intensity value of a gene from the test value. Please help me by explaining which of the above two kinds of values are appropriate for calculating pearson correlation coefficients of all Vs all genes.
I am trying to do a microarray analysis on a time-series (5 time points) gene expression (GE) data of 3000 genes. I want to calculate all Vs all (3000 Vs 3000 genes') Pearson correlation coefficient (PCC) values. I searched a lot in literature and found that studies use values that are 'Log (base 2) of the ratio of the median of test spot's intensity to median of control's intensity'.
The intensity values are already normalised (background normalised). Whereas, some studies subtract the control GE intensity value of a gene from the test value. Please help me by explaining which of the above two kinds of values are appropriate for calculating pearson correlation coefficients of all Vs all genes.