Entering edit mode
6.3 years ago
Pol
▴
70
Hi,
When I work with microarrays i normally analyze differential expression comparing between two conditions (tumor and normal).
I wonder if it's possible to obtain differential expression with only one condition (tumor). I mean, can I select a gene (or a set of genes) and obtain which genes are increased or decreased with respect to this gene? How?
Thanks
I mean, you could, but that would indicate that you do have two conditions (or at least expect expect to). Are you looking for differences in subtypes of your tumors or those treated with a certain drug?
Thank you very much for the reply. I do not have two conditions, the problem is that I work with samples on which it is very difficult to obtain good control, in fact, there isn’t a good control for them. What I wanted to know is how certain genes are in my samples and for that reason I thought I could compare them, for example, respect to a housekeeping gene.
That's what Z-scores will tell you. Convert your normalised log base 2 expression values to the Z-scale and then you can see genes that are 1, 2, 3, et cetera, standard deviations from the mean (Z-scores indicate standard deviations from the mean).
Alternatively, just pick your gene that you believe to be the 'reference' level and then compare all others to it individually via a simple Students' t-tests.
Thank you very much for the reply. Z-scores look like very interesting I will look into it.
Z-scores are a good idea - I'd take it a step further and suggest using modified z-scores, which utilize the median rather than the mean and aren't nearly so heavily affected by outliers as a standard z-score.
You can read more about them here.