Question: How to get data from GEO by using getGEO function ?
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gravatar for 11818480
11 months ago by
118184800
118184800 wrote:

Hello everyone,

I am using R package GEOquery to get a geo object from file ( in my directory) by getgeo function. I already download the required packages

BiocManager::install("DESeq2")
BiocManager::install("limma")
BiocManager::install("GEOquery")

library(DESeq2)
library(limma)
library(Biobase)
library(GEOquery)

I used this code and get this message

getGEO("GPL96.annot.txt.gz")

Using locally cached version of GPL96.ANNOT.TXT.GZ found here:
C:\Users\MTECH~1\AppData\Local\Temp\RtmpsHinCo/GPL96.ANNOT.TXT.GZ.soft 
Error in parseGSEMatrix(fname, destdir = destdir, AnnotGPL = AnnotGPL,  : 
  parsing failed--expected only one '!series_data_table_begin'

could anyone help me because I am beginner in R , please ?

rna-seq R • 806 views
ADD COMMENTlink modified 11 months ago by zx87549.9k • written 11 months ago by 118184800
GEO A character string representing a GEO object for download and parsing. (eg., 'GDS505','GSE2','GSM2','GPL96')

Can you try:

getGEO("GPL96")
ADD REPLYlink modified 11 months ago • written 11 months ago by GenoMax96k
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