Question: how to let readSummaries() use the correct directory to read allele information
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gravatar for hd48
3.0 years ago by
hd480
hd480 wrote:


Hi, 

Good afternoon. I ran into some big trouble when using readSummaries() function to read my previous output.

Previously I used the following code to read .cel files

library(oligo)
library(genomewidesnp6Crlmm)
setwd("X:/RESULTS/me")

celFiles <- list.celfiles(path=dir,full.names=T) #dir is the folder where the .cel files are instored
outdir <- "X:/RESULTS/me"
crlmm(celFiles,outdir) 

Recently I moved these results to another computer, under the directory of "I:/data/me"

Now I need to read these results and I use the following code to do it. Before the moving, these code works. The only differece is the directory outdir1.

outdir1 <- "I:/data/me"
alleleA <- readSummaries("alleleA",outdir1) 

Surprisingly, the R immediately gave the following error code

> alleleA <- readSummaries("alleleA",outdir1)
opening ff X:/RESULTS/me/alleleA-155429de1549.ff
Error: file.access(filename, 0) == 0 is not TRUE

It looks like these results remembered where they were created and want to be found in the same place. Since the crlmm step is too long (take me about one week), It is not possible for me to re-read it. Can anyone give me a clue how to make the program use the correct directory to do the job?

Your help is highly appreciated.

Matt

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