Question: Getgeo Error - line 1 did not have 6 elements
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Entering edit mode
6.1 years ago
jimmy_zeng ▴ 90

It's my first Question.

Hope someone can help me to solve that problem.

Why I can download GEO data by getGEO(R bioconductor package: GEOquery) in linux, but success in Window ??

It's very interesting that I can run it successfully in my Windows computer, but only failed in Linux server.

>GSE = "GSE1009"
>GPL = "GPL8300"
> data.series = getGEO(GEO = GSE, AnnotGPL = FALSE, getGPL = FALSE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/ Error in > scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :  **> line 1 did not have 6 elements**

I know what's wrong with it, But I don't know how to solve that problem. It should be "\t" to be delim I have try other study ID , failed also in linux server.

I guess I should use Option() to set some parameter , but I really don't know how

Thank you in advance !!!

> data.series = getGEO(GEO = GSE, AnnotGPL = FALSE, getGPL = FALSE)
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 6 elements
>sessionInfo()


R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:

[1] GEOquery_2.32.0     Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):

[1] bitops_1.0-6   RCurl_1.95-4.8 tools_3.1.1    XML_3.98-1.4

but In Windows:

> GSE = "GSE1009"
> data.series = getGEO(GEO = GSE, AnnotGPL = FALSE, getGPL = FALSE)

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/
Found 1 file(s)
GSE1009_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/GSE1009_series_matrix.txt.gz'
downloaded 225 KB
> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252   LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] GEOquery_2.34.0     Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):

[1] tools_3.2.2    RCurl_1.95-4.8 bitops_1.0-6   XML_3.98-1.4  
> 
GEO bioconductor firewall linux scan • 4.3k views
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