Search
Question: clusterprofiler enrichment analysis geneList argument: duplicate 'row.names' (entrezID) are not allowed?
0
gravatar for akleens1
9 days ago by
akleens10
akleens10 wrote:

I have problems with the geneList argument for the enrichment Analysis of clusterprofiler. The example GeneList from the DOSE package shows a descending ordered vector of logFC with entrezID as names().


If I try to construct that from my toptable output I face a problem because several different probenames match the same entrezID which results in an error when I try to assign entrezID row.names : “Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed”.


topTableOut is output from limma topTable.

to sort by logFC, toptable sort.by = "logFC" does not work since sorting is done on absolute numbers, therefore

topTableOut_geneList <- topTableOut[sort(topTableOut[,"logFC"], index.return= TRUE, decreasing = TRUE)$ix,]

 

# to replace rownames probeID by EntrezID, hgug8x60kv2ENTREZID is probe to entrezID translation from the package hgug8x60kv2.db Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray which I have built with AnnotationForge
rownames(topTableOut_geneList) <- unlist(mget(rownames(topTableOut_geneList),hgug8x60kv2ENTREZID, ifnotfound = NA))


Is there any other way to do a valid GeneList from tobTable Output if several probes are mapping to the same entrezID? I was not able to find any further documentation about what is allowed for GeneList and how flexible it is.

The overrepresentation statistics are not affected by this.

Session info
 setting  value                     
 version  R version 3.4.2 (2017-09-28)
 system   x86_64, mingw32           
 ui       Rgui                      
 language (EN)                      
 collate  German_Germany.1252       
 tz       America/New_York          
 date     2017-11-08                

Packages
 package         * version  date       source      
 annotate          1.56.0   2017-10-31 Bioconductor
 AnnotationDbi   * 1.40.0   2017-10-31 Bioconductor
 backports         1.1.1    2017-09-25 CRAN (R 3.4.1)
 base            * 3.4.2    2017-09-28 local       
 Biobase         * 2.38.0   2017-10-31 Bioconductor
 BiocGenerics    * 0.24.0   2017-10-31 Bioconductor
 BiocParallel    * 1.12.0   2017-10-31 Bioconductor
 bit               1.1-12   2014-04-09 CRAN (R 3.4.1)
 bit64             0.9-7    2017-05-08 CRAN (R 3.4.1)
 bitops            1.0-6    2013-08-17 CRAN (R 3.4.1)
 blob              1.1.0    2017-06-17 CRAN (R 3.4.1)
 checkmate         1.8.5    2017-10-24 CRAN (R 3.4.2)
 clusterProfiler * 3.6.0    2017-10-31 Bioconductor
 colorspace        1.3-2    2016-12-14 CRAN (R 3.4.1)
 compiler          3.4.2    2017-09-28 local       
 data.table        1.10.4-3 2017-10-27 CRAN (R 3.4.1)
 datasets        * 3.4.2    2017-09-28 local       
 DBI               0.7      2017-06-18 CRAN (R 3.4.1)
 devtools        * 1.13.3   2017-08-02 CRAN (R 3.4.2)
 digest            0.6.12   2017-01-27 CRAN (R 3.4.1)
 DO.db             2.9      2017-11-06 Bioconductor
 DOSE            * 3.4.0    2017-10-31 Bioconductor
 dotCall64       * 0.9-04   2016-10-07 CRAN (R 3.4.2)
 fastmatch         1.1-0    2017-01-28 CRAN (R 3.4.1)
 fgsea             1.4.0    2017-10-31 Bioconductor
 fields          * 9.0      2017-06-06 CRAN (R 3.4.2)
 genefilter      * 1.60.0   2017-10-31 Bioconductor
 ggplot2           2.2.1    2016-12-30 CRAN (R 3.4.1)
 glue              1.2.0    2017-10-29 CRAN (R 3.4.2)
 GO.db           * 3.4.2    2017-11-06 Bioconductor
 GOSemSim          2.4.0    2017-10-31 Bioconductor
 graph             1.56.0   2017-10-31 Bioconductor
 graphics        * 3.4.2    2017-09-28 local       
 graphite          1.24.0   2017-10-31 Bioconductor
 grDevices       * 3.4.2    2017-09-28 local       
 grid            * 3.4.2    2017-09-28 local       
 gridExtra         2.3      2017-09-09 CRAN (R 3.4.1)
 gtable            0.2.0    2016-02-26 CRAN (R 3.4.1)
 hgug8x60kv2.db  * 1.0.0    2017-09-16 Bioconductor
 httr              1.3.1    2017-08-20 CRAN (R 3.4.2)
 igraph            1.1.2    2017-07-21 CRAN (R 3.4.2)
 IRanges         * 2.12.0   2017-10-31 Bioconductor
 lattice           0.20-35  2017-03-25 CRAN (R 3.4.2)
 lazyeval          0.2.1    2017-10-29 CRAN (R 3.4.2)
 limma           * 3.34.0   2017-10-31 Bioconductor
 magrittr          1.5      2014-11-22 CRAN (R 3.4.1)
 maps            * 3.2.0    2017-06-08 CRAN (R 3.4.2)
 Matrix            1.2-11   2017-08-21 CRAN (R 3.4.2)
 matrixStats       0.52.2   2017-04-14 CRAN (R 3.4.1)
 memoise           1.1.0    2017-04-21 CRAN (R 3.4.1)
 methods         * 3.4.2    2017-09-28 local       
 mgcv            * 1.8-22   2017-09-19 CRAN (R 3.4.2)
 Mulcom          * 1.28.0   2017-10-31 Bioconductor
 munsell           0.4.3    2016-02-13 CRAN (R 3.4.1)
 nlme            * 3.1-131  2017-02-06 CRAN (R 3.4.2)
 org.Hs.eg.db    * 3.4.2    2017-11-05 Bioconductor
 parallel        * 3.4.2    2017-09-28 local       
 pkgconfig         2.0.1    2017-03-21 CRAN (R 3.4.1)
 plyr              1.8.4    2016-06-08 CRAN (R 3.4.1)
 purrr             0.2.4    2017-10-18 CRAN (R 3.4.2)
 qvalue            2.10.0   2017-10-31 Bioconductor
 R6                2.2.2    2017-06-17 CRAN (R 3.4.1)
 rappdirs          0.3.1    2016-03-28 CRAN (R 3.4.2)
 RColorBrewer    * 1.1-2    2014-12-07 CRAN (R 3.4.1)
 Rcpp              0.12.13  2017-09-28 CRAN (R 3.4.2)
 RCurl             1.95-4.8 2016-03-01 CRAN (R 3.4.1)
 reactome.db       1.62.0   2017-11-06 Bioconductor
 ReactomePA      * 1.22.0   2017-10-31 Bioconductor
 reshape2          1.4.2    2016-10-22 CRAN (R 3.4.1)
 rlang             0.1.4    2017-11-05 CRAN (R 3.4.2)
 RSQLite           2.0      2017-06-19 CRAN (R 3.4.1)
 rstudioapi        0.7      2017-09-07 CRAN (R 3.4.2)
 rvcheck           0.0.9    2017-07-10 CRAN (R 3.4.1)
 S4Vectors       * 0.16.0   2017-10-31 Bioconductor
 scales            0.5.0    2017-08-24 CRAN (R 3.4.1)
 spam            * 2.1-1    2017-07-03 CRAN (R 3.4.2)
 splines           3.4.2    2017-09-28 local       
 stats           * 3.4.2    2017-09-28 local       
 stats4          * 3.4.2    2017-09-28 local       
 stringi           1.1.5    2017-04-07 CRAN (R 3.4.1)
 stringr           1.2.0    2017-02-18 CRAN (R 3.4.1)
 survival          2.41-3   2017-04-04 CRAN (R 3.4.2)
 sva             * 3.26.0   2017-10-31 Bioconductor
 tibble            1.3.4    2017-08-22 CRAN (R 3.4.1)
 tidyr             0.7.2    2017-10-16 CRAN (R 3.4.2)
 tools             3.4.2    2017-09-28 local       
 utils           * 3.4.2    2017-09-28 local       
 withr             2.1.0    2017-11-01 CRAN (R 3.4.2)
 XML               3.98-1.9 2017-06-19 CRAN (R 3.4.1)
 xtable            1.8-2    2016-02-05 CRAN (R 3.4.1)

ADD COMMENTlink modified 9 days ago by Guangchuang Yu800 • written 9 days ago by akleens10
0
gravatar for Guangchuang Yu
9 days ago by
Hong Kong
Guangchuang Yu800 wrote:
several different probenames match the same entrezID

maybe mean/median value of these probes to assign to the corresponding EntrezID.

ADD COMMENTlink written 9 days ago by Guangchuang Yu800
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 118 users visited in the last hour