What Do I Need To Know About My Microarray Experiment In Order To Do Normalization On It?

Question

[KCC]

I originally asked how to process some microarray data, but sounds like don't know enough to process my data yet.

The situation is that I have some data coming on a microarray experiment performed in 2007.

All I have is a table of numbers and some anecdotal information that it's probably in log scale. Looking at it, it seems to be log scale. I was able to find out that it's agilent and the species is C.elegans.

I want to figure out which genes are overexpressed and which are underexpressed.

It seems that to do this I need to get more information about the chip. So, what do I need to know about the microarray chip used, before I can start my analysis?

Edit: I realized it was dumb of me not to list what information I have in my file. I was assuming these types of files must be standard.

The file contains transcript IDs and a number next to each. I believe the number is a measurement of each transcript expression level and I've been told this is in a log scale.

[Neilfws]

You asked a similar question already which was deleted - I guess by you. It appears that you do not know which array platform was used, which makes analysis rather difficult if not impossible.

[KCC]

Yeah. I asked how to do the normalization, but based on your answers, I realized I needed to take a step back and ask what information I needed before I could even start talking about normalization.

[Neilfws]

Can you post a few of the transcript IDs?

Answer 1

[Josh Herr]

I'm not clear on what information you have and what you still need for the analysis. First thing I would do is make sure you know what the probes are in each location of your array. There should be a matrix file provided by the chip manufacturer (do you know this information?) with at the very least the probe ID and sequence, this depends on the version of the array.

[Josh Herr]

Thanks for updating the original post, can you still be a little more clear? Do you know which chip you have, not just Agilent, but which version: you need to figure out what probe is printed where.

[KCC]

I edited my post to indicate, that my file contains transcript IDs and expression values in a log scale. So, my problems are related mapping transcripts back to the genes and coming up with a single number for the level of expression of the gene.

[Sean Davis]

Can you give examples of the transcript IDs?