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16 months ago by
mmayo0
mmayo0 wrote:

Hi,

I'm attempting to download the datasets that go with the paper "Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group" but I am having some difficulty with the R package GEOQuery.

There are two datasets (stage 1 and 2) associated with the research paper, and the and I've been using these commands to download them both:

>library(GEOquery)
>library(foreign)

>u <- getGEO('GSE13204')

Unfortunately I get this error:

Welcome to Bioconductor

Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('GEOquery.inmemory.gpl'=FALSE)
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE13nnn/GSE13204/matrix/
OK
Found 2 file(s)
GSE13204-GPL570_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE13nnn/GSE13204/matrix/GSE13204-GPL570_series_matrix.txt.gz'
Content type 'application/x-gzip' length 886530886 bytes (845.5 MB)
==================================================

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
invalid 'nlines' argument
In addition: There were 50 or more warnings (use warnings() to see the first 50)

The warnings are all identical:

> warnings()
Warning messages:
1: In readLines(fname) : line 1 appears to contain an embedded nul
2: In readLines(fname) : line 216 appears to contain an embedded nul

etc

I currently have no idea whether this is problem with the data or the R package. Can anyone help?