Question: GEOquery getGeo line 1 didn't have 6 elements
1
gravatar for jianwang2010
4.2 years ago by
jianwang201010
jianwang201010 wrote:

Dear GEOquery users/developers:

I encountered an error while using GEOquery package to download GSExxx from GEO database.  Googled and saw similar error messages posted by others but no suitable solutions seem available.  

Any help is greatly appreciated.

This is the R code:
===================
library(Biobase)
library(GEOquery)
  
gse <- "GSE49279"
gset <- try(getGEO(gse, GSEMatrix =TRUE, getGPL=FALSE))

The error message:
=================
Setting options('download.file.method.GEOquery'='curl')
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9105/matrix/
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 6 elements
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49279/matrix/
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 6 elements

Here is my sessionInfo()

R version 3.1.2 (2014-10-31)

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     RCurl_1.95-4.3      Biobase_2.26.0     
 [4] BiocGenerics_0.12.0 nza_3.0.1           rpart_4.1-8        
 [7] arules_1.1-5        Matrix_1.1-4        XML_3.98-1.1       
[10] ca_0.55             MASS_7.3-35         e1071_1.6-4        
[13] tree_1.0-35         nzr_3.0.1           bitops_1.0-6       
[16] RODBC_1.3-10       
geoquery error message • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Sean Davis21k • written 4.2 years ago by jianwang201010

This GSE Series Matrix file has no data in it, so using getGEO on the GSEMatrix file will not get you anything except the annotation.  

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Sean Davis21k

It might be because that is an RNA-Seq analysis. There doesn't appear to be any data in the matrix.txt.gz file - it just has pointers to the SRA.

!Sample_supplementary_file_1    "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX328/SRX328505" "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX328/SRX328506" "ftp://ftp-tra"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX328/SRX328582"
!series_matrix_table_begin
"ID_REF"        "GSM1196555"    "GSM1196556"    "GSM1196557"    "GSM1196558"    "GSM1196559"    "GSM1196560"    "GSM1196561"    "GSM1196562"    "GSM1196563"    "GSM1196564"    "GSM1196565"    "GSM1196566"    "GSM1196567"  "GSM1196632"
!series_matrix_table_end
ADD REPLYlink written 4.2 years ago by James W. MacDonald50k

This is handled by recent versions of GEOquery and shouldn't result in an error.  I need to check on when I made that change.  In any case, an update to the newest version of R is likely a good idea.

ADD REPLYlink written 4.2 years ago by Sean Davis21k
> z <- getGEO("GSE49279")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49279/matrix/
Found 1 file(s)
GSE49279_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  7275  100  7275    0     0   4959      0  0:00:01  0:00:01 --:--:--  4962
File stored at:
/data3/tmp/RtmpoaoxiB/GPL11154.soft

> head(exprs(z[[1]]))
     GSM1196555 GSM1196556 GSM1196557 GSM1196558 GSM1196559 GSM1196560
     GSM1196561 GSM1196562 GSM1196563 GSM1196564 GSM1196565 GSM1196566
     GSM1196567 GSM1196568 GSM1196569 GSM1196570 GSM1196571 GSM1196572
     GSM1196573 GSM1196574 GSM1196575 GSM1196576 GSM1196577 GSM1196578
     GSM1196579 GSM1196580 GSM1196581 GSM1196582 GSM1196583 GSM1196584
     GSM1196585 GSM1196586 GSM1196587 GSM1196588 GSM1196589 GSM1196590
     GSM1196591 GSM1196592 GSM1196593 GSM1196594 GSM1196595 GSM1196596
     GSM1196597 GSM1196598 GSM1196599 GSM1196600 GSM1196601 GSM1196602
     GSM1196603 GSM1196604 GSM1196605 GSM1196606 GSM1196607 GSM1196608
     GSM1196609 GSM1196610 GSM1196611 GSM1196612 GSM1196613 GSM1196614
     GSM1196615 GSM1196616 GSM1196617 GSM1196618 GSM1196619 GSM1196620
     GSM1196621 GSM1196622 GSM1196623 GSM1196624 GSM1196625 GSM1196626
     GSM1196627 GSM1196628 GSM1196629 GSM1196630 GSM1196631 GSM1196632

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] 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_3.2.0    RCurl_1.95-4.5 bitops_1.0-6   XML_3.98-1.1  
>

 

ADD REPLYlink written 4.2 years ago by James W. MacDonald50k
> z2 <- getGEOSuppFiles("GSE49279")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49279/suppl/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  117k  100  117k    0     0  62190      0  0:00:01  0:00:01 --:--:-- 62190

> zz <- read.delim("GSE49279/GSE49279_miRNAseq-processed_data.txt.gz")
> head(zz)
            miRNA   ACC1   ACC2  ACC4   ACC5   ACC6   ACC8  ACC9  ACC10 ACC11
1 hsa-let-7a-2-3p      0      4     0      6      3      8     0      0     2
2   hsa-let-7a-3p    409    211    42    709    276    235   236    154   141
3   hsa-let-7a-5p 319828 296528 81039 347538 154576 161409 79395 120927 97828
4   hsa-let-7b-3p   1095    496   164    482    635    573   198    184   200
5   hsa-let-7b-5p  37840  46670  9304  78156  16937  14733  7407   5467 10759
6      hsa-let-7c   4326  17294  8150  16537   7958   6738  1377   4102  1409

 

ADD REPLYlink written 4.2 years ago by James W. MacDonald50k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 289 users visited in the last hour