Duplicate genes/different probes in micorray analyzes

Question

[Joe Kherery]

Hello everyone, I would like to know if it's correct delete duplicate genes that have the value of LogFC similiar (up or down).

I understand that each one is a different probe.

and what should I do when one probe is up and the other downregulated?

Regards,

[russhh]

I don't see an example of a probe-level disparity in this, could you highlight it

[Joe Kherery]

Dear russhh,

In my example I have only duplicate genes that follow the same direction of expression, but I have already seen results of a probe-level disparity.

So my questions are: 1. When I have "duplicate genes" that follow the same expression direction for different probes, can I delete one and keep the one with the highest expression? or what should I do?

1. And in cases of a probe-level disparity, a probe up and another downregulated what should I do?

Answer 1

[h.mon]

Disparity between probes may have an interesting underlying biological cause: it could indicate different isoforms of a gene have opposing patterns of variation at your experiment. You could try to map probes to exons to gather more information than the mapping to of probe to gene can convey. See seidel suggestion at Question: Differentially expressed genes.

edit: some more discussions and a paper.

Handling Duplicate Probe Expression Values In Spotted Cdna Microarray

https://support.bioconductor.org/p/90980/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1784106/

[Joe Kherery]

Thank you so much, It was of great importance.