R error: unable to find an inherited method for function ‘exprs’ for signature ‘"list"’
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Entering edit mode
2.6 years ago

Hi

I get this error in exprs

>DataSeries = getGEO("GSE5847", GSEMatrix = T, AnnotGPL = T, 
                    destdir = "D:/Microarray Data/sharifi.data" )
>expressionData = exprs(DataSeries)
>Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘exprs’ for signature ‘"list"’

How can i fix it?

microarray GEOquery • 2.3k views
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4
Entering edit mode
2.6 years ago
ATpoint 81k

The DataSeries itself is a list object, so do DataSeries$GSE5847_series_matrix.txt.gz to get the actual ExpressionSet which you can call exprs on.

It is a list because sometimes a GSE accession can contain multiple ExpressionSets, e.g. when the GSE is a SuperSeries such as https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13204 with (in case of that example) two SubSeries, so each SubSeries would then be one list element. I assume getGEO outputs a list even if only one ExpressionSet is present to be consistent in terms of output format.

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