Question: (Closed) Error in runing GEOquery package
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gravatar for villayatgoba
17 months 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 • 466 views
ADD COMMENTlink written 17 months ago by villayatgoba0

Hello villayatgoba!

We believe that this post does not fit the main topic of this site.

Duplicate posting

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

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ADD REPLYlink written 17 months ago by genomax65k
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