Question

GOexpress - Error when plotting expression data

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atorson • 0

@atorson-22788

Last seen 4.7 years ago

I’m analyzing a pair of RNA-seq datasets at the moment and am using GOexpress for ranking of GO terms and plotting. I am able to load in all of my data, conduct the analyses, and view the results but am having issues with the plotting. I am able to run the code in the vignette in its entirety. I’m happy to provide any other info that you might need.

However, when I run the following code (or any of the plotting functions), I continue to get the following error message:

heatmap_GO(go_id = "GO:0006869", result = cpb_fb_go_bp, eSet=expression_set) 

Error in if (any(gene_labels == "") & !NA.names) { :    missing value where TRUE/FALSE needed 

In addition: Warning message: In brewer.pal(n = length(unique(pData(eSet)[, f])), name = row.col.palette) :   minimal value for n is 3, returning requested palette with 3 different levels

My session info:

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

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

other attached packages:
[1] dplyr_0.8.3         GOexpress_1.16.1    Biobase_2.42.0      BiocGenerics_0.28.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3           plyr_1.8.5           RColorBrewer_1.1-2   pillar_1.4.3         compiler_3.5.1       prettyunits_1.1.1   
 [7] bitops_1.0-6         tools_3.5.1          progress_1.2.2       biomaRt_2.38.0       digest_0.6.23        bit_1.1-15.1        
[13] tibble_2.1.3         RSQLite_2.2.0        memoise_1.1.0        lifecycle_0.1.0      gtable_0.3.0         pkgconfig_2.0.3     
[19] rlang_0.4.3          DBI_1.1.0            rstudioapi_0.10      stringr_1.4.0        httr_1.4.1           caTools_1.17.1.2    
[25] gtools_3.8.1         S4Vectors_0.20.1     vctrs_0.2.2          IRanges_2.16.0       hms_0.5.3            tidyselect_1.0.0    
[31] stats4_3.5.1         bit64_0.9-7          glue_1.3.1           R6_2.4.1             AnnotationDbi_1.44.0 XML_3.99-0.3        
[37] gdata_2.18.0         purrr_0.3.3          ggplot2_3.2.1        blob_1.2.1           magrittr_1.5         gplots_3.0.1.2      
[43] scales_1.1.0         randomForest_4.6-14  assertthat_0.2.1     colorspace_1.4-1     KernSmooth_2.23-15   stringi_1.4.5       
[49] lazyeval_0.2.2       RCurl_1.98-1.1       munsell_0.5.0        crayon_1.3.4

RNA-seq transcriptomics gene ontology gene expression GOexpress • 1.3k views

ADD COMMENT • link updated 4.9 years ago by kevin.rue ▴ 350 • written 4.9 years ago by atorson • 0

score 0 · Answer 1 · 2020-01-28

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Entering edit mode

kevin.rue ▴ 350

@kevinrue-6757

Last seen 7 months ago

University of Oxford

Hi Alex,

Have you checked that the genes associated with the GO term are present in your dataset? i.e., what is the output of the following?

list_genes(go_id="GO:0006869", result= cpb_fb_go_bp, data.only=TRUE)

Best Kevin

ADD COMMENT • link 4.9 years ago kevin.rue ▴ 350

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Yes, they're present in the dataset. Here is the output of the code:

[1] LDEC022952-RA LDEC000097-RA LDEC000096-RA LDEC000098-RA LDEC000099-RA LDEC024456-RA LDEC016635-RA LDEC021824-RA LDEC021823-RA
[10] LDEC010610-RA LDEC001465-RA LDEC016750-RA LDEC001773-RA LDEC018332-RA LDEC015007-RA LDEC024718-RA LDEC011029-RA
18694 Levels: LDEC000001-RA LDEC000002-RA LDEC000003-RA LDEC000004-RA LDEC000005-RA LDEC000006-RA LDEC000007-RA LDEC000008-RA ... LDEC024838-RA

ADD REPLY • link 4.9 years ago atorson • 0

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Entering edit mode

As a workaround, can you please try the following:

heatmap_GO(go_id = "GO:0006869", result = cpb_fb_go_bp, eSet=expression_set, gene_names=FALSE)

This will use the original gene identifier instead of trying to replace it with the gene name.

Separately, as an attempt to understand the issue, can you give me the result of

colnames(cpb_fb_go_bp$genes)

In particular, there should be a column named "external_gene_name". It already happened in the past that Ensembl renamed that column in their database, causing issues in GOexpress because I hard-coded it. If that turns out to be the issue again I'll parameterise it.

ADD REPLY • link 4.9 years ago kevin.rue ▴ 350

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Entering edit mode

Apologies for the slight delay on the response. When setting gene_names=FALSE I am able to produce the plot.

To your second point - the result of colnames(cpb_fb_go_bp$genes)produces this:

> colnames(cpb_fb_go_bp$genes)
[1] "Score"              "Rank"               "external_gene_name"

ADD REPLY • link 4.9 years ago atorson • 0