Error when Creating Expression Set from Geo Set
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Entering edit mode
dmm204 • 0
@dmm204-15412
Last seen 3.6 years ago

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 • 698 views ADD COMMENT 1 Entering edit mode @james-w-macdonald-5106 Last seen 15 hours ago United States 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)
featureData
featureNames: 1 2 ... 36480 (36480 total)
fvarLabels: ID UG cluster ORF SPOT_ID
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.
0
Entering edit mode
dmm204 • 0
@dmm204-15412
Last seen 3.6 years ago

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!