microarray_notes.md

Microarray Notes

Multiple Probes Per Gene

Description of how to handle multiple probes per gene:

• https://www.reddit.com/r/bioinformatics/comments/544zqi/multiple_probes_for_one_gene/d7zpcxj/?utm_source=share&utm_medium=web2x

What the at, s_at, and x_at mean at the end of probe set IDs:

• https://www.biostars.org/p/16093/
• https://dintor.eurac.edu/doc/doc/HSGeneAtlas.html
• https://cbdm.uni-mainz.de/files/2016/02/GE_microarrays.pdf

Selecting The Optimal Probe

The jetset package identifies the best probe to represent each gene for a select number of microarray platforms. These probes were selected based on quality/precision for the specific gene. Very useful package.

Handling Unannotated Probes

Sometimes the microarray platform on GEO will be missing transcript/gene annotations. EBI provides an overview of how to annotate these probes.

• See if probe mappings are provided by ENSEMBL in the BioMart portal - look for the platform type in the Attributes section
• If probe mappings do not already exist, there are several re-annotation tools that will align the probe sequence to the genome and determine the best matching gene. This approach will require more work as better to look for pre-existing annotations if possible