GEOquery returning NAs as probe names
1
1
Entering edit mode
John ▴ 30
@dfe35d7a
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

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] 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
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
John ▴ 30
@dfe35d7a
Last seen 1 day ago
United States

Dev was notified on github and has submitted a fix!

ADD COMMENT

Login before adding your answer.

Traffic: 504 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6