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rloopsinputbioconductor

Creating a loop to use read.eset in bioconductor

I would like to create a loop to load this files through read.esetof bioconductor. I tried that:

for(k in 1:29){
  expr <- paste0("/home/proj/MT_Nellore/R/eBrowser/Adjusted/LRRadjustedextremes0.5kgchr",k,".txt")
  pdat <- paste0("/home/proj/MT_Nellore/R/eBrowser/Adjusted/Samplesbinary0.5.txt")
  ffdat <- paste0("/home/proj/MT_Nellore/R/LRR/Chr_adjusted/probeslabeladjustedchr",k,".txt")
  eset <- read.eset(exprs.file="expr", pdat.file="/home/proj/MT_Nellore/R/eBrowser/Adjusted/Samplesbinary0.5.txt", fdat.file="ffdat")
 }

However I get this error:

## Error in file(file, "r") : cannot open the connection
## In addition: Warning message:
## In file(file, "r") : cannot open file 'ffdat': No such file or directory

Any suggestions?

Solution

  • Ah - just spotted the error - you must remove quotes from around the "ffdat" on the final line, and same for the "expr"