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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:UsersPeterAppDataLocalTempRtmpwRdSpO/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

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