Error when using getgeodata

Hello,

When I try this example to import GEO series data, I get an error that Matlab is "Unable to find data for the specified GEO Accession Number."

https://www.mathworks.com/help/bioinfo/examples/working-with-geo-series-data.html

When I try with the dataset I am hoping to download, I get the exact same error.

However, when I try: geoStruct = getgeodata('GSM1768') .... this seems to work.

Is the issue with GSE series?

Thank You,

Vitaly

[Tim DeFreitas]

Can you share the exact command that you are running that is giving you the erorr? I am able to retrieve the GSE data in the example:

>> gseData = getgeodata('GSE5847', 'ToFile', 'GSE5847.txt')

gseData = 

  struct with fields:

    Header: [1×1 struct]
      Data: [22283×95 bioma.data.DataMatrix]

Answer 1

[Vitaly Kheyfets]

Hi Tim,

That's strange. This is what I'm getting:

Thanks,

Vitaly

>> gseData = getgeodata('GSE5847', 'ToFile', 'GSE5847.txt')
Error using getgeodata (line 156)
Unable to find data for the specified GEO Accession Number. Recently
submitted data sets might not be available for immediate download. 

[Tim DeFreitas]

What version of Matlab are you using? If you have an older version, you are likely running into this: https://www.mathworks.com/support/bugreports/2175385

[Vitaly Kheyfets]

Yup, I'm using 2018b. Thanks!!!

Vitaly