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

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
• 4,930 views • link
written by raavi21198 • raavi21198

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.

• 0 views • link
written by cpad0112 cpad0112

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

• 0 views • link
written by raavi21198 • raavi21198

Hello raavi21198!

We believe that this post does not fit the main topic of this site.

error resolved

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by raavi21198 • raavi21198

2 answers

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

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written by raavi21198 • raavi21198

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.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

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

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written by raavi21198 • raavi21198

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

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written by ATpoint ATpoint

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