Entering edit mode
4.7 years ago
mi_kappa
•
0
Hello all,
I have a normalized microarray dataset (affy_hg_u133_plus_2) of 23100 genes and 582 individuals. I have been in a discussion about filtering my dataset on absolute gene expression levels by looking into whether Y chromosome genes are expressed in the female individuals in my dataset. Y chromosome genes should not be expressed in women thus expression values can be reflective of background noise. The idea is to take the mean Y chromosome gene expression in women and below that it will be background noise and above that we will have the final expressed dataset. I have three questions:
- Is this step necessary to my analysis?
- If it is would that be the way to go or there are other analysis that I could use?
- if we filter as I describe above does it make sense to use the mean? I feel the median would be more appropriate.
Thank you for your help!