GEOquery
0
0
Entering edit mode
@d27aed9d
Last seen 6 weeks ago
Germany

Hi,

I want to access a GEO dataset and I followed the instructions here: https://sbc.shef.ac.uk/geo_tutorial/tutorial.nb.html When I want to see the expression data exprs(gse) I only get the GSMs and there is a logical class output. I then downloaded the _RAW.rar of the GEO and constructed a phenotype/metadata table with the individual GSMs (.tab.gz.) as rownames. Is there an easy way to create a matrix table from the pheontype/metadata table I've constructed, without the need to manually load the individual GSMs?! In this example this was done with library(affy) for CEL files: https://www.stat.purdue.edu/bigtap/online/docs/Introduction_to_Microarray_Analysis_GSE15947.html - however this library doesn't apply to my files, which are RNA seq files (.tab.gz.)

Thank you very much!

GEOquery • 106 views
ADD COMMENT
0
Entering edit mode

Hi, could you tell us the GEO accession number of the dataset you need ? thanks

ADD REPLY

Login before adding your answer.

Traffic: 290 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6