GEOquery returning NAs as probe names
Entering edit mode
John ▴ 30
Last seen 1 day ago
United States

I am re-running old code to obtain microarray datasets with GEOquery. However, after not running the same code for a month or so, I am getting a new error. I am now getting NAs as probe names for datasets using getGEO(). It seems that datasets obtained with platform GPL4372 are having issues but platform GPL2700 is not.

Edit: It was working previously when GEOquery was still using readr. After the new update is when I am getting the NAs issue.

#This is returning NAs
gset <- getGEO("GSE33000", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL4372", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
fData(gset) #returning NAs

> fData(gset)
        ID Gene title Gene symbol Gene ID UniGene title UniGene symbol UniGene ID Nucleotide Title GI GenBank Accession Platform_CLONEID Platform_ORF Platform_SPOTID
NA    <NA>       <NA>        <NA>    <NA>          <NA>           <NA>       <NA>             <NA> NA              <NA>               NA         <NA>            <NA>
NA.1  <NA>       <NA>        <NA>    <NA>          <NA>           <NA>       <NA>             <NA> NA              <NA>               NA         <NA>            <NA>
NA.2  <NA>       <NA>        <NA>    <NA>          <NA>           <NA>       <NA>             <NA> NA              <NA>               NA         <NA>            <NA>

#This works fine
gset <- getGEO("GSE15222", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL2700", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
fData(gset) #This returns annotation
> fData(gset)
                         ID                                                         Gene title Gene symbol Gene ID UniGene title UniGene symbol UniGene ID
GI_10047089-S GI_10047089-S                                     small muscle protein, X-linked        SMPX   23676                                        
GI_10047091-S GI_10047091-S                                                       transgelin 3      TAGLN3   29114                                        
GI_10047093-S GI_10047093-S                      heat shock protein family A (Hsp70) member 14      HSPA14   51182   

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readr_2.1.0            GEOquery_2.62.1        Biobase_2.54.0         BiocGenerics_0.40.0    EnhancedVolcano_1.12.0 ggrepel_0.9.1          ggplot2_3.3.5         

loaded via a namespace (and not attached):
 [1] beeswarm_0.4.0      tidyselect_1.1.1    purrr_0.3.4         ggrastr_1.0.1       colorspace_2.0-2    vctrs_0.3.8         generics_0.1.1      utf8_1.2.2         
 [9] rlang_0.4.12        R.oo_1.24.0         pillar_1.6.4        glue_1.5.0          withr_2.4.2         DBI_1.1.1           R.utils_2.11.0      bit64_4.0.5        
[17] ggalt_0.4.0         RColorBrewer_1.1-2  lifecycle_1.0.1     cellranger_1.1.0    munsell_0.5.0       gtable_0.3.0        R.methodsS3_1.8.1   tzdb_0.2.0         
[25] extrafont_0.17      vipor_0.4.5         curl_4.3.2          fansi_0.5.0         Rttf2pt1_1.3.9      Rcpp_1.0.7          KernSmooth_2.23-20  scales_1.1.1       
[33] BiocManager_1.30.16 limma_3.50.0        bit_4.0.4           proj4_1.0-10.1      hms_1.1.1           dplyr_1.0.7         ash_1.0-15          grid_4.1.2         
[41] tools_4.1.2         magrittr_2.0.1      maps_3.4.0          tibble_3.1.6        crayon_1.4.2        extrafontdb_1.0     tidyr_1.1.4         pkgconfig_2.0.3    
[49] MASS_7.3-54         ellipsis_0.3.2      data.table_1.14.2   xml2_1.3.2          ggbeeswarm_0.6.0    rstudioapi_0.13     assertthat_0.2.1    R6_2.5.1           
[57] compiler_4.1.2
GEOquery • 161 views
Entering edit mode

Should be fixed in release and devel, versions 2.62.2 and 2.63.2, respectively. Thanks for the bug report.

Entering edit mode
John ▴ 30
Last seen 1 day ago
United States

Dev was notified on github and has submitted a fix!


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