Question: Query About Data Of Breast Cancer Dataset
gravatar for Zhe Liu
9.5 years ago by
Zhe Liu40
Zhe Liu40 wrote:

Dear all,

I have a problem in dealing with a classic breast cancer dataset from the following paper.

A gene-expression signature as a predictor of survival in breast cancer

I downloaded data from here. But when I do the visualization of probe signal, it seems that data has not been normalized and they usually appear around zero which is on the contrary to normal data with mean around 7 (after log2 transformation). I have noticed that this array chip is not standard one and the authors developed by themselves. So I wonder what kind of data processing method should be performed to make the analysis meaningful.

BTW, where could I obtain some documentation for this array data expect read me files accompanied with array matrix from download site. For example, I met a problem in understanding the header of the array data.

"Substance Gene Log Ratio Log Ratio Error p-Value Intensity Flag"

I am not quite sure if it is OK to adopt Log Ration as the signal value, while as for Log Ratio Error p-Value and Intensity, what do they mean?

Thanks a lot and I am looking forward your reply.

Zhe Liu

microarray cancer • 2.3k views
ADD COMMENTlink written 9.5 years ago by Zhe Liu40
gravatar for Sean Davis
9.5 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

These data are from a two-color array. You can do some reading on the subject, but two-color arrays were (and to a certain extent) still are a common array design. The Log Ratio column is the column that you would use as the signal and usually represents a log2 ratio of the tumor intensity at each spot to that of a "reference" sample. Two-color array normalization methods include median-centering or loess normalization, though there are others. Having a mean/median for each array near or at zero implies that some normalization might have been done.

If you have detailed questions about these data (after reading the paper), a good place to start is to email the corresponding author.

ADD COMMENTlink written 9.5 years ago by Sean Davis26k

Hi Sean, Thanks a lot for your soon reply!

ADD REPLYlink written 9.5 years ago by Zhe Liu40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1515 users visited in the last hour