I have a list of DE gene symbols that I want to convert to entrez gene ids so I can compare the output from different experiments.
Previously I used the following code to do this with no issues.
v8 <- data.frame(c("5.20", "74.44", "46.67", "26.94", "22.25", "15.13", "2.27", "8.05", "5.11", "2.75", "18.95"), c("HSPB1", "ENTPD5", "CLU", "THBD", "RRM2", "FAH", "EZR", "H2-L", "ACAA2", "SERPINB1A", "FABP4"))
names(v8)[1] <- "Max_Fold_Change"
names(v8)[2] <- "HGNC_Symbol"
mart <- useMart(biomart = "ensembl", dataset = "cgchok1gshd_gene_ensembl")
#obtain entrez gene ids for each gene name in the progenesis dataset (v8) and store in a dataframe v10
V10=getBM(attributes = c("external_gene_name", "entrezgene_id", "hmmpanther"),
filters = "external_gene_name",
values = v8$HGNC_Symbol,
bmHeader = T, mart = mart)
Today I get the following error.
cannot open compressed file 'C:\Users\Peter\AppData\Local\Temp\RtmpwRdSpO/biomaRt_ac6442011a322c53ec8e6fb374c8cd4a.rds', probable reason 'No such file or directory'
I'm not clear why there's a temporary file being called or how to replace it if that turns out to be required.
Any suggestions would be welcomed.
Peter
3 answers
This is a local problem very much unrelated to this forum... probably something to do with permissions or your local machine (did you try turning it off and then back on again?).
> V10=getBM(attributes = c("external_gene_name", "entrezgene_id", "hmmpanther"), filters = "external_gene_name", values = v8$HGNC_Symbol, bmHeader = TRUE, mart = mart)
> V10
Gene name NCBI gene (formerly Entrezgene) ID PANTHER ID
1 Acaa2 100765829 PTHR18919
2 Acaa2 100765829 PTHR18919:SF145
3 Rrm2 100752542 PTHR23409
4 Rrm2 100752542 PTHR23409:SF20
5 Thbd 100765076 PTHR24036
6 Thbd 100765076 PTHR24036:SF5
7 Hspb1 100763481 PTHR45640
8 Hspb1 100763481 PTHR45640:SF7
9 Fabp4 100760812 PTHR11955
10 Fabp4 100760812 PTHR11955:SF83
11 Entpd5 NA PTHR11782
12 Entpd5 NA PTHR11782:SF35
13 Clu 100756447 PTHR10970
14 Clu 100756447 PTHR10970:SF1
15 Ezr NA PTHR23281
16 Ezr NA PTHR23281:SF13
17 Fah 100757944 PTHR43069
18 Fah 100757944 PTHR43069:SF2
>
When you run a query biomaRt creates a temporary copy of the results as an rds file. It does this because large queries are actually submitted in batches, and it's sometimes useful to have access to the results from early batches in the case that something goes wrong with a late batch. It looks like the file causing the error is one of these temporary files.
However biomaRt should clear all the temporary files once a query has completed successfully. Also it should not attempt to read such a file without checking that it exists firsts, so I'm not sure how it's ending up at the error you're seeing.
Perhaps the simplest approach is to close the R session and start again. This should deleted the entire R temporary folder and create a fresh one. Please report back if you continue to run into the issue and we'll try to track down what's causing it.
@mike smith, I had tried closing the r session and starting again but hadn't rebooked my machine. @benformatics, a reboot did the trick. Thanks, v much.
Peter
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