Question: Standardised to a mean of 0 and standard deviation 1
1
gravatar for skjobs0123
13 months ago by
skjobs012370
skjobs012370 wrote:

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.

R • 623 views
ADD COMMENTlink modified 13 months ago by ATpoint38k • written 13 months ago by skjobs012370
2

what did you try already ?

ADD REPLYlink written 13 months ago by Nicolas Rosewick9.0k

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

ADD REPLYlink written 13 months ago by skjobs012370

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

ADD REPLYlink written 13 months ago by RamRS30k
3
gravatar for ATpoint
13 months ago by
ATpoint38k
Germany
ATpoint38k wrote:

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).

ADD COMMENTlink modified 13 months ago by RamRS30k • written 13 months ago by ATpoint38k

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

ADD REPLYlink written 13 months ago by skjobs012370
1

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

ADD REPLYlink written 13 months ago by RamRS30k
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