Question: NCBI analyze dataset
0
gravatar for lvitale
23 months ago by
lvitale0
lvitale0 wrote:

I downloaded the following dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68928

and read the file using getGEO function.

multicancer <- getGEO(filename='Data/multicancer.soft.gz')

like here https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/

A this point how I can extract phenodata ed expressionData from the "multicancer" object?

if I try to get expression set using

eset <- GDS2eSet(multicancer, do.log2=TRUE)

I had this error:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘Table’ for signature ‘"GSE"’

Because the class of "multicancer" variable is "GSE".

Thank you so much!

biobase geoquery R ncbi • 645 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by lvitale0
1
  • Please use the code formatting to present your post better
  • Please use appropriate tags, just R doesn't really make sense, you're using a few packages and databases, mention them
ADD REPLYlink written 23 months ago by RamRS30k
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