Question: Error when Creating Expression Set from Geo Set
0
gravatar for dmm204
19 months ago by
dmm2040
dmm2040 wrote:

Hello! 

I am currently using the Geoquery package to analyze a Geo dataset. I was successfully able to download the series matrix, but receive an error message when creating an expression set from the data. Below, is the error I receive. Any help would be appreciated to help fix the error. 

gse111581<-getGEO('GSE111581',GSEMatrix=TRUE)
Found 1 file(s)
GSE111581_series_matrix.txt.gz
Using locally cached version: /var/folders/rl/nh27_qnx0_q4xgksvhzd6knc0000gn/T//RtmpPE8J7y/GSE111581_series_matrix.txt.gz
Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_integer()
)
See spec(...) for full column specifications.
|============================================================================================================================================| 100%    5 MB
Using locally cached version of GPL24704 found here:
/var/folders/rl/nh27_qnx0_q4xgksvhzd6knc0000gn/T//RtmpPE8J7y/GPL24704.soft 
B
> show(gse111581)
$GSE111581_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 36480 features, 24 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM3034545 GSM3034546 ... GSM3034568 (24 total)
  varLabels: title geo_accession ... treatment:ch1 (50 total)
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 36480 (36480 total)
  fvarLabels: ID UG cluster ORF SPOT_ID
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL24704 

> show(pData(phenoData(gse111581[[1]]))[1:5,c(1,6,8)])
               title type source_name_ch1
GSM3034545  D1-C1-0h  RNA        D1-C1-0h
GSM3034546  D1-C1-4h  RNA        D1-C1-4h
GSM3034547  D1-C1-8h  RNA        D1-C1-8h
GSM3034548 D1-C1-24h  RNA       D1-C1-24h
GSM3034549  D2-C1-0h  RNA        D2-C1-0h
> eset <- GDS2eSet(gds,do.log2=TRUE)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘Table’ for signature ‘"list"’

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bindrcpp_0.2.2      GEOquery_2.46.15    Biobase_2.38.0      BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     tidyr_0.8.0      dplyr_0.7.4      assertthat_0.2.0 R6_2.2.2         magrittr_1.5     pillar_1.2.1     stringi_1.1.7   
 [9] rlang_0.2.0      curl_3.2         limma_3.34.9     xml2_1.2.0       tools_3.4.4      readr_1.1.1      glue_1.2.0       purrr_0.2.4     
[17] hms_0.4.2        compiler_3.4.4   pkgconfig_2.0.1  tidyselect_0.2.4 bindr_0.1.1      tibble_1.4.2    

Thank you very much! 

Best, 

Deena Maurer 

Graduate Student, University of Pittsburgh 

geoquery • 329 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by dmm2040
Answer: Error when Creating Expression Set from Geo Set
1
gravatar for James W. MacDonald
19 months ago by
United States
James W. MacDonald52k wrote:

You should more closely read the output that you have posted above. In particular this part:

> show(gse111581)
$GSE111581_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)    <- like especially this line
assayData: 36480 features, 24 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM3034545 GSM3034546 ... GSM3034568 (24 total)
  varLabels: title geo_accession ... treatment:ch1 (50 total)
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 36480 (36480 total)
  fvarLabels: ID UG cluster ORF SPOT_ID
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL24704 

Which tells you that the first item of your gse111581 object is an ExpressionSet! And do note that there is a help page for the function that you have used, which you should always consult first, since it's helpful and stuff. From ?getGEO

Value:

     An object of the appropriate class (GDS, GPL, GSM, or GSE) is
     returned.  If the GSEMatrix option is used, then a list of
     ExpressionSet objects is returned, one for each SeriesMatrix file
     associated with the GSE accesion.  If the filename argument is
     used in combination with a GSEMatrix file, then the return value
     is a single ExpressionSet.
ADD COMMENTlink written 19 months ago by James W. MacDonald52k
Answer: Error when Creating Expression Set from Geo Set
0
gravatar for dmm204
19 months ago by
dmm2040
dmm2040 wrote:

Thanks for the response, James! That all makes sense - I am new to r and the package, GEOQuery, so at first I wasn't sure what the output meant, but taking a closer look I see that the Expression set was created. Thank you again for the advice! 

ADD COMMENTlink written 19 months ago by dmm2040
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