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analyzing cel files

Dear bioinformaticians

i have to deal with .cel files for the first time from Chip Snp sequencing

the purpose is to get a matrix with positions to do population genomics after

i've heard about R packages but i dont know which on is the best for me

or maybe any pipeline , thank you for your tips

chip snp
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updated by benformatics benformatics • written by scipio04 • scipio04

What have you tried?

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written by Ram Ram

affy package but i have errors with justRMA() and readaffy() functions :

" Is /home/alambard/celfiles/ABCDE.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats"

and :

"Error in read.celfile.header(filenames[[1]]) : "

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written by scipio04 • scipio04

Show us your exact code please.

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written by Ram Ram

i juste settled R to the working directory where i have cel files located

and tried c <- Readaffy() and c <- justRMA() as the documentation says

library(affy)
setwd ("home/usr/celfiles")
list.files ( pattern = ".CEL") 
c <- Readaffy()

and then the error come

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updated by Ram Ram • written by scipio04 • scipio04

Which documentation are you referring to? I'm sure no documentation would ask you to:

  1. Run ReadAffy() with no arguments
  2. Assign the output to a variable sharing name with one of the most popular R functions (c()).
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written by Ram Ram

Thanks, I was mistaken about point #1. Please note that you're running Readaffy() and not ReadAffy() - R is case sensitive.

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written by Ram Ram

yes , i just misstyping it but i ran ReadAffy()

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written by scipio04 • scipio04

I see. In that case, from your error message, the ABCDE.CEL file doesn't seem to be what the program expects. Maybe look for a sample Affy dataset that works and compare those CEL files with yours?

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written by Ram Ram

i tried with example file from affy but still same error

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written by scipio04 • scipio04

ok i go take a look on it , thank you

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written by scipio04 • scipio04

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