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?
p.s here is an example of the annotation I am looking for. I downloaded supplementary info of a paper:
Yes its from Trinity! Thank you for clarification on the first question. The GEO annotations still only give Probe ID & circRNA. I will use separate annotations from published papers and use the Probe ID as a key. Oh and I'd like to thank you for the numerous tutorials/tips you have posted on here, I have used them countless times!
Sure thing - happy to help out a fellow Irishman!