Standardised to a mean of 0 and standard deviation 1

Question

[skjobs]

How to normalize the data set in R using the "Standardized to a mean of 0 and standard deviation 1"? I have a TCGA expression data and want to normalized like above equations. Please write code of R if possible.

[Nicolas Rosewick]

what did you try already ?

[skjobs]

I was trying to normalized the different transcriptomics expression such as miRNA, mRAN and mutations data.

[Ram]

And how did you try to normalize them? What did you use?

Answer 1

[ATpoint]

It means transforming data to the Z-score aka standard score. The Z-score indicates how much a value deviates from the mean across all values and by this is a relative measure of e.g. gene expression, fold changes, whatever you put in. In R the scale function can do that for you, e.g. t(scale(t(matrix))) where matrix is the expression matrix with columns = samples and rows = genes. Data should be appropriately normalized, e.g. log2(normalized counts) with normalized counts e.g. coming from the DESeq2 or edgeR normalization or from transformations such as vst or rlog (the latter two already on log scale so no need to log them again).

[skjobs]

Mean of 0 and standard deviation 1 is it means Z-Score of normal distribution?

[Ram]

The wikipedia page says exactly that, look at the image.