.SOFT file (GEO) equivalent on ArrayExpress

Question

[christophe.morin]

Hello there,

I'm currently doing an internship trying to analyze ChIP-chip by tiling array data from Saccharomyces cerevisiae.

I have a task which is to try and find the equivalent of the .SOFT files available on GEO for another database, ArrayExpress. After a bit of math, ArrayExpress contains more data on the specified subject and my team wants to use its data to develop a pipeline (details irrelevant here).

SOFT files contain the platform (GPL), the samples (GSM) and the series (GSE) and would be very convenient for what I'm trying to achieve but they are not accessible from the ArrayExpress database.

Does an equivalent even exist? I've been searching for quite a while and only found the data in separated files.

Thanks in advance for helping me out,

Chris

[Sean Davis]

ArrayExpress uses MageTab files. https://www.ebi.ac.uk/arrayexpress/help/magetab_spec.html

Answer 1

[Sean Davis]

While I am not answering your question directly, you might want to take a look at the ArrayExpress package for R:

https://bioconductor.org/packages/ArrayExpress

[christophe.morin]

Thanks a lot for this quick reply.

I'm looking into it right now!