Question: how to calculate the log2 median-centered intensity in onconmine
0
gravatar for Ming Lu
10 months ago by
Ming Lu10
Australia
Ming Lu10 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?

ADD COMMENTlink modified 10 months ago by The160 • written 10 months ago by Ming Lu10
0
gravatar for The
10 months ago by
The160
United States
The160 wrote:

Sometimes, people use a "robust" estimation of SD along with the "robust" estimation of population mean, which is the median in this case( sometimes people use trimmed mean as well). For robust SD, often "median absolute deviation"(MAD) is used to calculate the robust z-score.

Please check whether median along with MAD (or any other robust estimates of mean and variance) was used by Oncomine

https://www.pnas.org/content/pnas/suppl/2012/11/30/1209673109.DCSupplemental/pnas.201209673SI.pdf

ADD COMMENTlink modified 10 months ago • written 10 months ago by The160

Hi The thanks I change the command to median_center_apply <- function(x) {apply(x, 2, function(y) (y - median(y))/mad(y))} but still not work

ADD REPLYlink written 10 months ago by Ming Lu10

Try the Iglewicz and Hoaglin formula:

y.z <- 0.6745 * (y-median(y,na.rm=TRUE))/mad(y)

https://www.itl.nist.gov/div898/handbook/eda/section3/eda35h.htm

ADD REPLYlink written 10 months ago by The160

thanks but sorry The still not work the oncomine value is larger than what I get, after times 0.6745, it became much larger.

ADD REPLYlink modified 10 months ago • written 10 months ago by Ming Lu10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1148 users visited in the last hour