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.
1 answer
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.
Can you give examples of the transcript IDs?
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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.
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.
Can you post a few of the transcript IDs?