unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
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@245f6648
Last seen 2 days ago
Canada

I am trying to get a table of GSE data I have but I get the following error:

"Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘Table’ for signature ‘"GSE"’ "

The code in R studio is this:

library(GEOquery)

gds <- getGEO(filename = "GSE7535_family.soft.gz")

geData <- Table(gds)

sessionInfo( )

R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] GEOquery_2.60.0 Biobase_2.52.0 BiocGenerics_0.38.0

loaded via a namespace (and not attached): [1] xml2_1.3.2 magrittr_2.0.1 hms_1.1.0 tidyselect_1.1.1
[5] R6_2.5.0 rlang_0.4.11 fansi_0.5.0 dplyr_1.0.7
[9] tools_4.1.0 utf8_1.2.1 DBI_1.1.1 ellipsis_0.3.2
[13] tibble_3.1.2 lifecycle_1.0.0 crayon_1.4.1 BiocManager_1.30.16 [17] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 vctrs_0.3.8
[21] glue_1.4.2 limma_3.48.1 compiler_4.1.0 pillar_1.6.1
[25] generics_0.1.0 pkgconfig_2.0.3 ```

GEOquery • 66 views
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Entering edit mode
@sean-davis-490
Last seen 15 days ago
United States

In your code above, gds is an ExpressionSet, not a GEODataset.

class(gds)

To learn more about an ExpressionSet object and how to use it:

help("ExpressionSet")

There is no Table method for an ExpressionSet object. To get a matrix of gene expression values, you could do:

geData=exprs(gds)
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