Hello,

I downloaded a dataset from the GEO at the NCBI and launched the following
commands:
> library(GEOquery)
> gse <- getGEO(filename="GSE25935_family.soft.gz")

Here is the error message I got:
Parsing....
Found 465 entities...
GPL4133 (1 of 465 entities)
GSM636943 (2 of 465 entities)
...
GSM637180 (239 of 465 entities)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
 :
  scan() expected 'an integer', got '5.845752745'
Calls: getGEO ... .parseGSMWithLimits -> fastTabRead -> read.delim ->
read.table -> scan

Is the input file badly formatted?

Thanks for any help,
TF

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GEOquery_2.19.4 Biobase_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.5-0 XML_3.2-0

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