Question: Error in runing GEOquery package
0
gravatar for villayatgoba
2.2 years ago by
villayatgoba0 wrote:

My system information is given below

> sessionInfo ()
> 
> R version 3.3.2 (2016-10-31)

> Platform: x86_64-pc-linux-gnu (64-bit)
> 
>Running under: Ubuntu 17.04

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

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base   

other attached packages:

 [1] hugene10sttranscriptcluster.db_8.5.0 hugene10stprobeset.db_8.5.0         
 [3] org.Hs.eg.db_3.4.0                   hugene10stv1probe_2.18.0            
 [5] AnnotationDbi_1.36.2                 IRanges_2.8.2                       
 [7] S4Vectors_0.12.2                     hugene10stv1cdf_2.18.0              
 [9] gcrma_2.46.0                         affy_1.52.0                         
[11] GEOquery_2.40.0                      Biobase_2.34.0                      
[13] BiocGenerics_0.20.0                  BiocInstaller_1.24.0

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.13          XVector_0.14.1        splines_3.3.2        
 [4] zlibbioc_1.20.0       bit_1.1-12            R6_2.2.2             
 [7] rlang_0.1.4           blob_1.1.0            httr_1.3.1           
[10] tcltk_3.3.2           tools_3.3.2           DBI_0.7              
[13] digest_0.6.12         bit64_0.9-7           tibble_1.3.4         
[16] preprocessCore_1.36.0 affyio_1.44.0         bitops_1.0-6         
[19] RCurl_1.95-4.8        memoise_1.1.0         RSQLite_2.0          
[22] Biostrings_2.42.1     XML_3.98-1.9          pkgconfig_2.0.1      
>

I am following a work flow to do gene expression analysis from BioConductor packages. during my analysis i go through the source("http://bioconductor.org/biocLite.R") and biocLite("GEOquery") command but, during the command of sapply I am getting the following error message

 `getGEOSuppFiles("GSE10329")`

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl/

OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl//GSE10329_RAW.tar'
Content type 'application/x-tar' length 122982400 bytes (117.3 MB)
==================================================
downloaded 117.3 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE10nnn/GSE10329/suppl//filelist.txt'
Content type 'text/plain' length 1389 bytes
==================================================
downloaded 1389 bytes

`untar("GSE10329/GSE10329_RAW.tar", exdir="data")`

> > cels = list.files("data/", pattern = "CEL")

> sapply(paste("data", cels, sep="/"), gunzip)

Error in FUN(X[[i]], ...) : 

  Argument 'filename' and 'destname' are identical: data/GSM261030.CEL

> cels = list.files("data/", pattern = "CEL")

> sapply(paste("data", cels, sep="/"), gunzip)

Error in FUN(X[[i]], ...) : 

  Argument 'filename' and 'destname' are identical: data/GSM261030.CEL

> cels = list.files("data/", pattern = "CEL")
geoquery R • 913 views
ADD COMMENTlink modified 2.2 years ago by Hussain Ather940 • written 2.2 years ago by villayatgoba0

Assuming that you are going to be processing the .CEL files with Bioconductor tools, there is no reason to gunzip them at all. Packages for reading .CEL files can usually read them in the gzipped format.

ADD REPLYlink written 2.2 years ago by Sean Davis25k
1
gravatar for Hussain Ather
2.2 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

According to the GEOQuery code for gunzip, gunzip works by replacing ".gz" of the file to be unzipped with "" to get the destname from filename. You need to make sure the file you are using gunzip on is a .tar.gz file.

ADD COMMENTlink written 2.2 years ago by Hussain Ather940
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