I have downloaded raw data from GSE118959. The platform used for this study was '074301 Arraystar Human CircRNA microarray V2 -- Agilent Technologies'.
In terms of Agilent circRNA microarray data, firstly, does anyone know if biomaRt has the annotations? Heres whats available when searching "Agilent" in mart atributes:
My second attempt was to look at the list of circRNAs provided by the GEO study which looks like this:
My main confusion comes from the fact that:
1) there are 9757 probeIDs in this file, yet roughly 15600 lines in the raw microarray file. Are there multiple duplicates/controls?
2) the 'Alias' column has plenty of missing values, which is irritating considering the names used in 'Alias' are in other circRNA databases - using these databases to annotate would result in numerous annotations.
Does anyone have experience in annotating these circRNA probes?