How to tell gains and losses from a CGH Microarray Dataset

Question

[doncheng1]

Hi Guys,

I am quiet new to this, I have a CGH dataset which I downloaded from NCBI GEO and from this I just want to know how I am able to tell whether there was a gain or a loss. There is a normalised log2ratio column which I believe is indicating the cy3/cy5 ratio. Below is a snapshot of the data.

Help will be quiet appreciated. My question is by looking at this data, how do you tell which one is a gain or a loss and at which location did the gain occur. Again the data was generated from an Agilent Microarray.

[Jonathan Crowther]

I cant get your image so if you could post it as a link?

[doncheng1]

Hi Jonathan,

here is the link to the image:

https://drive.google.com/file/d/0B8Cwsroe0eKcajdfVHBPQlBSR1k/edit?usp=sharing

Answer 1

[Jonathan Crowther]

Excellent,

I would first suggest reading this

There is a really nice summary about the data.It should help you!

How did you generate the data as I would read the LogRatio to be the Cy5/Cy3 which is your Exp/Ref ratio. But you will have to check if it is in Log2Ratio or just the LogRatio to make sure you are calling correctly.

The "SystematicName" looks like the position of the oligo's that are giving this ratio so I would think it is there.

Again this is dependent on what software you have used for analysis.

Answer 2

[doncheng1]

Thanks Jonathan,

I got already generated data from NCBI GEO. I think they calculated the log2 ratio from Cy5/Cy3.

Thanks