GETGEODATA problems, any suggests?

I am writing you for a problem that I found today while I was retrieving the data from ncbi geo with the getgeodata Matlab function.

In particular, I looked to download the data of bacteria transcriptome filtering the ‘Study Type’ for ‘Expression profiling by high throughput sequencing’ in GEO Datasets. Every studies which I selected to download with the Matlab function getgeodata gave me null results (if try to download the sample within the series, GSM, Matlab gave me the warning: ‘Warning: Problems reading the GEO data. The structure may be incomplete.’). For example, if I try to download the Series: ‘GSE19115’ (Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing) via ftp the download ends correctly, instead, the Matlab structure downloaded is empty. This problems repeats every time that I tried to download a Datasets from this collection of studies. Differently, selecting (‘Expression profiling by array’) I can download with Matlab function getgeodata every data I desire.

Thank you in advance,

Best,

Davide

Answer 1

[Arthur Goldsipe]

I believe the problem is that the records for these samples do not contain any actual data tables. For example, if you look at GSM473848 (the first sample for GSE19115), you will see that raw data is not provided for this record. The functions were not designed for these kinds of records.