Question: MILES dataset download
gravatar for mmayo
11 months ago by
mmayo0 wrote:


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:


>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('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 2 file(s)
trying URL ''
Content type 'application/x-gzip' length 886530886 bytes (845.5 MB)
downloaded 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


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



ADD COMMENTlink modified 11 months ago by shepherl ♦♦ 620 • written 11 months ago by mmayo0
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