Question: Error When Reading GEO Series Matrix File Using GEOquery in R
1
gravatar for Alonzo
3.3 years ago by
Alonzo10
United States
Alonzo10 wrote:

I'm running R 3.2.3 on Windows 8, trying to get phenotype data from a GSE using GEOquery (v. 2.36.0), but when I run the command

GSE781 <- getGEO(filename="GSE781--GPL96_series_matrix_txt.gz", GSEMatrix = TRUE)

I get the following error:

Error in xj[i]: only 0's may be mixed with negative subscripts

In addition: Warning message: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : downloaded length 1278353 != reported length 200.

I get the same "Error in xj[i]: only 0's may be mixed with negative subscripts" error when I tried using

GSE781 <- getGEO("GSE781", GSEMatrix = TRUE)

I'm really stumped as to what I could be doing wrong. Any help is much appreciated!

ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 3.3 years ago by Alonzo10
1

The following worked for me:

GSE781 <- getGEO("GSE781", GSEMatrix = TRUE)

GEOquery_2.36.0
R version 3.2.1
ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by informatics bot570
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