Arraystar Human CircRNA microarray V2 annotation

Question

[Barry Digby]

Hey all,

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?

Best, Barry

p.s here is an example of the annotation I am looking for. I downloaded supplementary info of a paper:

Answer 1

[Kevin Blighe]

Hey Barry,

Looks like a study from Trinity? There is a more appreciable number of probes in the official GEO record for this array, HERE, which I believe covers the ~15000 to which you refer. Many of the ones that you see in the raw files are also going to be control probes.

I don't believe there is annotation for this in biomaRt, as it appears to be a custom array.

The author-provided Excel file probably contains the probes used after filtering. Losing a few thousand probes based on QC is actually common enough in microarray studies.

Kevin

[Barry Digby]

Hi Kevin,

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!

Best,

Barry

[Kevin Blighe]

Sure thing - happy to help out a fellow Irishman!