clusterProfiler: enrichDavid produces NA values
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n.kreim ▴ 20
@nkreim-7374
Last seen 7.6 years ago
Germany
<html lang="en">

Hi,

I have an issue using the enrichDavid function for clusterProfiler. It returns a NA values if there is a pvalue cutoff or a qvalue cutoff.

david = enrichDAVID(gene=david.genes,
        idType="ENTREZ_GENE_ID",
            minGSSize=3,
            listType="Gene",
            annotation="GOTERM_BP_ALL",
            pvalueCutoff=1,
            qvalueCutoff=1,
            david.user = "email@email.com")

> tableis.na(summary(david)$ID))

FALSE
  165

> table(summary(david)$pvalue < 0.05)

FALSE  TRUE
  148    17

> david = enrichDAVID(gene=david.genes,
+ idType="ENTREZ_GENE_ID",
+ minGSSize=3,
+ listType="Gene",
+ annotation="GOTERM_BP_ALL",
+ pvalueCutoff=0.05,
+ qvalueCutoff=1,
+ david.user = "email@email.com")

> table(is.na(summary(david)$ID))

TRUE
 165

Does anyone have any idea how to solve this issue? I can take the results of the first comparison and filter myself but it may be better to know what is causing that behaviour.

 

 

Here is the sessionInfo:

R version 3.3.1 (2016-06-21)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Arch Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                  LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8       LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8      LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RDAVIDWebService_1.10.0 org.Ce.eg.db_3.3.0      BiocInstaller_1.22.3    biomaRt_2.28.0          clusterProfiler_3.0.4  
 [6] DOSE_2.10.7             GOSemSim_1.30.3         ggplot2_2.1.0           gplots_3.0.1            RColorBrewer_1.1-2     
[11] GOstats_2.38.1          graph_1.50.0            Category_2.38.0         Matrix_1.2-6            AnnotationDbi_1.34.4   
[16] IRanges_2.6.1           S4Vectors_0.10.2        Biobase_2.32.0          BiocGenerics_0.18.0    

loaded via a namespace (and not attached):
 [1] igraph_1.0.1           rJava_0.9-8            DBI_0.4-1              gdata_2.17.0           genefilter_1.54.2     
 [6] bitops_1.0-6           RBGL_1.48.1            GSEABase_1.34.0        lattice_0.20-33        qvalue_2.4.2          
[11] RSQLite_1.0.0          GO.db_3.3.0            stringr_1.0.0          gtools_3.5.0           SparseM_1.7           
[16] xtable_1.8-2           Rcpp_0.12.6            plyr_1.8.4             DO.db_2.9              tools_3.3.1           
[21] RCurl_1.95-4.8         annotate_1.50.0        AnnotationForge_1.14.2 scales_0.4.0           assertthat_0.1        
[26] gtable_0.2.0           KernSmooth_2.23-15     stringi_1.1.1          reshape2_1.4.1         caTools_1.17.1        
[31] munsell_0.4.3          grid_3.3.1             XML_3.98-1.4           colorspace_1.2-6       topGO_2.24.0          
[36] magrittr_1.5           splines_3.3.1          survival_2.39-5        tidyr_0.5.1            matrixStats_0.50.2    
[41] tibble_1.1      

Thanks.

Best

Nastasja 

clusterProfiler • 1.4k views
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1
Entering edit mode
n.kreim ▴ 20
@nkreim-7374
Last seen 7.6 years ago
Germany

Hi Guangchuang,

Thank you.

this explains why the numbers do not match. The numbers do match up if I filter for the padjust. Then the amount of NAs rows matches the amount of rows which are filtered out.

I would be great  the information that the filtering is done for adjusted p values to the documentation.

Best,

Nastasja

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0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 days ago
China/Guangzhou/Southern Medical Univer…
> table(summary(david)$pvalue < 0.05)

FALSE  TRUE
  148    17

 

 

clusterProfiler screen out the result by p.adjust < pvalueCutoff .

 

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