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