[BioC] getGEO

[Weiwei Shi]

hi,

I am a newbie using this GEOquery package and have a couple of issues
when I used it:

1. When I install it, there are two warnings, I think it could be
specific to my Mac and should be ok. But I just want to confirm here.

2. When I used
getGEO("GSE3210")
then there is a kind of connection problem. I am wondering how to correct this?

3. When I download the gz file and run it locally,
it seems working but ends with a couple of warnings (shown below). Is it ok?

4. BTW, it is really slow, even running from local. Should gunzipping
at first help?

The details of running can be seen from below. Thanks a lot!

Weiwei

> biocLite("GEOquery")
Running getBioC version 0.1.8 with R version 2.3.1
Running biocinstall version 1.8.5 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3/GEOquery_1.7.2.tgz'
Content type 'application/x-gzip' length 135676 bytes
opened URL
==================================================
downloaded 132Kb


The downloaded packages are in
	/tmp/RtmpnbgyQZ/downloaded_packages
Warning messages:
1: number of rows of result
	is not a multiple of vector length (arg 2) in: cbind(1, res0,
Repository = repos)
2: cannot create HTML package index in: make.packages.html()

> t0 <- getGEO("GSE3210")
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE3210/GSE3210_family.soft.gz'
Error in download.file(myurl, destfile, mode = mode) :
	cannot open URL
'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE3210/GSE3210_family.soft.gz'

> t0 <- getGEO(filename="../data/GSE3210_family.soft.gz")

Warning messages:
1: input string 1 is invalid in this locale in: grep.perl(pattern, x,
ignore.case, value, useBytes)
2: input string 8592 is invalid in this locale in: grep.perl(pattern,
x, ignore.case, value, useBytes)
3: input string 8592 is invalid in this locale in: grep.perl(pattern,
x, ignore.case, value, useBytes)
4: input string 8592 is invalid in this locale in: grep.perl(pattern,
x, ignore.case, value, useBytes)
5: input string 8592 is invalid in this locale in: grep.perl(pattern,
x, ignore.case, value, useBytes)
6: input string 8592 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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---Matrix III