What exactly is in a microarray .pcl file?

[jambler]

Resolved

Hi all,

I am trying to export data from microarray experiments from the TBDB website, and one of the options is to download the data in .pcl format.

(Example link below)

http://www.tbdb.org/expressionHistory.shtml?gn=Rv0024

What I need is the fold change of expression for each gene from each experiment. But, when I download the .pcl file and look at the values, none of them are equal to the expression value, intensity, or significance I saw in the preview window.

What are the values contained in this file? Are they relative expression values? Have they undergone some form of normalisation when they were downloaded? None of the documentation on the TBDB site is clear on this.

Thanks!

[mastal]

File format help page from TBDB

http://www.tbdb.org/help/formats.shtml#pcl

[jambler]

Ah, thanks!

In general the pcl file will contain log-transformed data, which is needed for clustering to work properly.