Question: Z-scores from log2fold change
gravatar for writersblog02
4.6 years ago by
United States
writersblog0250 wrote:

Hi, I am learning to analyze microarray data and was wondering if you can calculate z-scores from log2fold change values in R

microarray • 3.5k views
ADD COMMENTlink modified 4.6 years ago by Benn8.1k • written 4.6 years ago by writersblog0250

The formula for Z-scores is pretty straight-forward (z <- (logratios - mean)/stddev) but it requires a mean and standard deviation that define the distribution of experimental error under the null hypothesis. But we can't know what the null hypothesis is without knowing more. Could you tell us a bit more about the data you're looking at?

ADD REPLYlink written 4.6 years ago by Vince FitzPatrick10
gravatar for Benn
4.6 years ago by
Benn8.1k wrote:

You can use the scale() function in R. It calculates z-score per column, so if you want z-scores from rows, you'll have to transpose first (and back afterwards).

transposed_matrix <- t(matrix)

z_tr_mt <- scale(transposed_matrix)

z_score <- t(z_tr_mt)
ADD COMMENTlink written 4.6 years ago by Benn8.1k
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