**10**wrote:

Does anyone know how to caculate log2 median-centered intensity in onconmine

the expression data x by GEOquery is gene probe in rows, sample/array in column.

I first log2 all data

1.

```
y <- log2(x)
```

then median centered and normalize sd to one per array/sample

2.

```
median_center_apply <- function(x) {apply(x, 2, function(y) (y - median(y))/sd(y))}
z <- median_center_apply(y)
```

(which seems like the z-score but between genes in one sample/column, not on one gene probe between samples in one row, anyone know why oncomine use log2 median-centered intensity but not z-score?）

However， i still cannot get the exact same number with that in oncomine. anyone can help?