problem in microarray data analysis

Question

[zizigolu]

hi,

I have about 300 CEL files in a folder like below

cels [1] "GSM359972.CEL.gz" "GSM359973.CEL.gz" "GSM359974.CEL.gz" "GSM359975.CEL.gz" [5] "GSM359976.CEL.gz" "GSM359977.CEL.gz" "GSM359978.CEL.gz" "GSM359979.CEL.gz" [9] "GSM359980.CEL.gz" "GSM359981.CEL.gz" "GSM359982.CEL.gz" "GSM359983.CEL.gz"

I am attempting to unzip them together but I cannot

sapply(paste("data", cels, sep="/"), gunzip)

Error in match.fun(FUN) : object 'gunzip' not found

but I don't know what I am doing wrong and googling too much I didn't find the solution

thank you

Answer 1

[Ar]

Are you using WIndows laptop/computer ? It seems gunzip is not installed. Anyways, you don't have to uncompress the files. You can directly read CEL.gz files using read.celfiles function using oligo package.

library(oligo)
path <- paste("data", cels, "/", sep="")
cels <- list.files(path = path, all.files = TRUE, pattern = "CEL")
cat("List of cell files: ",cels, "\n")

## reading the files and normalization
celfiles <- read.celfiles(filenames = paste(path,cels,sep = ""))

[zizigolu]

Yes right I am working with Windows8 laptop

thank you

[Mike]

same problem, as your previous post;

unpacking zipped file in R

[zizigolu]

yes today I faced the same problem which I faced 11 months ago...If I had tried to solve my problem 11 months ago today I had not to ask again...