R script for loading .CEL.gz files in afffy package
2
0
Entering edit mode
5 weeks ago
raavi21198 • 0

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)

R microarray data .CEL files affy package • 113 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
5 weeks ago
raavi21198 • 0

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

ADD COMMENT
2
Entering edit mode
5 weeks ago
Mensur Dlakic ★ 10k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

okay noted. thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 2336 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6