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)
