pathway analysis: ReactomePA and clusterProfiler

Question

[nsmaan]

Hello to Forum experts once again: I am trying the step-by-step document examples provided for reactomePA and clusterprofiler. Unfortunately i am stuck in the early steps itself.

To start, I am trying to run just a simple command line below, before i explore other advance options for pathway analysis (barplots, enrichment plots, etc.) on rna-seq data (Rattus n.) that i have

library(ReactomePA)
library(clusterProfiler)
x<-c("test.txt")
eg = bitr(x, fromType="SYMBOL", toType="GENENAME", OrgDb="org.Rn.eg.db")
head(eg)

but i get the error:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'GENENAME'.

---

The conversion of ENTREZID to GENENAME etc are also not working.

The top of my file (test.txt) looks like this:

ENSEMBL ENTREZID    SYMBOL  logFC   padj
ENSRNOG00000001115  288499  Slc29a4 -1.4677 0.005070498
ENSRNOG00000001656  170847  Kcnj15  -1.071107   0.009110337
ENSRNOG00000002212  305150  Hsd17b13    -1.168479   5.54E-07
ENSRNOG00000003020  299316  Slc25a47    -1.183244   0.000393189
ENSRNOG00000003977  114856  Dusp1   -1.386536   0.01449139
ENSRNOG00000004377  313977  Lpin1   -1.111481   0.000378619
ENSRNOG00000005871  60582   Il1rn   -1.294062   1.14E-05

Could someone please help? Thank you

[Ram]

Try converting the symbol column to uppercase, that will eliminate problems caused by case-sensitive querying in org.XX.eg.db

[nsmaan]

Thanks Ram. I tried

orgDb="org.RN.eg.db"
orgDb="org.Rn.eg.db"
OrgDb="org.RN.eg.db"
orgDb="org.Rn.eg.db"

But none of them working. I also reinstalled

BiocManager::install("org.Rn.eg.db", version = "3.8")

Any more suggestions that I can try please?

[Ram]

I think there's a misunderstanding - did you try:

Try converting the symbol column to uppercase

I was not talking about case sensitivity in org.XX.eg.db, I used the XX as a placeholder for organism.

[nsmaan]

My bad. Yes, i tried that too (in uppercase). When i try to read SYMBOL from my text file (shown in first post)

eg = bitr(x, fromType="SYMBOL", toType="GENENAME", OrgDb="org.Rn.eg.db")
Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'SYMBOL'.

OR (when i try to read ENSEMBL)

  None of the keys entered are valid keys for 'ENSEMBL' (when i try eg = bitr(x, fromType="ENSEMBL", toType="GENENAME", OrgDb="org.Rn.eg.db")

Answer 1

[Benn]

I think you need read.table instead of c to import your text file into R.

x <- read.table("test.txt", sep = "\t", header = T, stringsAsFactors = F)

eg <- bitr(x$SYMBOL, fromType="SYMBOL", toType="GENENAME", OrgDb="org.Rn.eg.db")

[nsmaan]

Thanks Ben!. This worked.

[Ram]

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