R script for loading .CEL.gz files in afffy package

Question

[raavi21198]

greetings to the members. I have to analyse miRNA (microarray data). i have downloaded the .CEL.gz files. however, i am unable to import them using affy for background normalisation. I am not sure which part have i missed. Kindly guide me Thanks a lot!

This is the R script i have used

library(affy)
#path to load CEL files
mirna <- "home/eshwari/Documents/GSE120356"
list.celfiles()
#import the files
datafiles <- ReadAffy(celfile.path = mirna)

this is the error I keep getting.

(Error in read.celfile.header(as.character(filenames[[1]])) : Is /home/eshwari/Documents/GSE120356/GSM3398822_N1.CEL.gz really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats)

[cpad0112]

can post the output from file /home/eshwari/Documents/GSE120356/GSM3398822_N1.CEL.gz in ubuntu/gnu-linux? If you have access to md5sum of the cel.gz, try using them.

[raavi21198]

I tried opening the file but it does'nt open in my system. And i need to analyse using R scripts only

Answer 1

[raavi21198]

Thankyou for your help!!. I could finally sort out the error. The file i was using was corrupted

Answer 2

[Mensur Dlakic]

The question seems pretty clear:

Is /home/eshwari/Documents/GSE120356/GSM3398822_N1.CEL.gz really a CEL file?

gunzip -tv /home/eshwari/Documents/GSE120356/GSM3398822_N1.CEL.gz

That command should give you a clear answer. It is possible that the file got corrupted during the download.

[raavi21198]

Okay Sir. Thank you so much. will make changes as mentioned.

[ATpoint]

The package can read gzip-compressed files, this is rather indication of corruption, try to re-download the file.

[raavi21198]

okay noted. thank you so much!