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I have two datasets of a given variable x that have the same length, let's say 14600 values in total each one.

I need to extract the extreme observations within each dataset, where extremes means values > 99th percentile.

I do this by using the R function quantile as follows, where df_1 and df_2 are the two datasets:

df_1_q99 = quantile(df_1$x, probs = 0.99)
df_1_extr = subset(df_1, x > df_1_q99[[1]])

df_2_q99 = quantile(df_2$x, probs = 0.99)
df_2_extr = subset(df_2, x > df_2_q99[[1]])

The issue, which does not make sense to me, is that for df_1 I obtain n=84 and for df_2 n=126 extreme values.

Shouldn't the number of extremes be the same since the two datasets have the same length?

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That is only true if each observation has a distinct value. When there are ties you can easily get the pattern you saw.

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