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,