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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)
mirna <- "home/eshwari/Documents/GSE120356"
list.celfiles()
#import the files


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
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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.

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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

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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

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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.

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Entering edit mode

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

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Entering edit mode

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

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Entering edit mode

okay noted. thank you so much!

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