[BioC] edgeR adding RefSeq IDs
Robin [guest]
guest at bioconductor.org
Mon Oct 21 15:23:34 CEST 2013
My pipeline for adding annotations suddenly didn't work, maybe because some packages are updated. Could you check if something is wrong with my pipeline, I loose all the rows when I add annotations:
> data <- read.table("~/Documents/Jobb/mRNA_Ch12/TreatedControlCounts.csv", row.names=1, sep="", header=T)
> head(data)
T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h C0h C0.25h C0.5h C1h C2h C3h
NM_001001130 68 95 56 43 66 62 68 90 63 89 65 85 58 49 81 49
NM_001001144 0 1 4 0 1 1 1 4 1 2 1 3 1 0 6 3
NM_001001152 79 129 52 50 24 45 130 154 112 147 56 85 67 33 52 31
NM_001001160 1 1 2 0 0 1 0 0 0 1 0 1 2 4 2 1
NM_001001176 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NM_001001177 1 3 2 3 0 1 1 0 2 0 1 6 4 1 3 0
C6h C12h C24h C48h
NM_001001130 76 73 48 77
NM_001001144 0 1 2 1
NM_001001152 93 77 65 109
NM_001001160 0 2 1 0
NM_001001176 0 0 0 0
NM_001001177 0 3 0 2
> y <- DGEList(counts=data[,1:20], genes=data[,0:1])
> library(org.Mm.eg.db)
> idfound <- rownames(y$genes) %in% mappedRkeys(org.Mm.egREFSEQ)
> y <- y[idfound,]
> dim(y)
[1] 0 20
> egREFSEQ <- toTable(org.Mm.egREFSEQ)
> m <- match(rownames(y$genes), egREFSEQ$accession)
> y$genes$EntrezGene <- egREFSEQ$gene_id[m]
> y$genes$Symbol <- egSYMBOL$symbol[m]
> m <- match(y$genes$EntrezGene, egSYMBOL$gene_id)
> y$genes$Symbol <- egSYMBOL$symbol[m]
> head(y$genes)
[1] genes EntrezGene Symbol
<0 rows> (or 0-length row.names)
-- output of sessionInfo():
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.4.0 limma_3.18.0 GSEABase_1.24.0
[4] annotate_1.40.0 org.Mm.eg.db_2.10.1 AnnotationForge_1.4.0
[7] org.Hs.eg.db_2.10.1 GOstats_2.28.0 graph_1.40.0
[10] Category_2.28.0 GO.db_2.10.1 RSQLite_0.11.4
[13] DBI_0.2-7 Matrix_1.0-14 lattice_0.20-24
[16] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] genefilter_1.44.0 grid_3.0.2 IRanges_1.20.0 RBGL_1.38.0
[5] splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2
[9] XML_3.98-1.1 xtable_1.7-1
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