analyzing cel files

Question

[scipio04]

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

[Ram]

What have you tried?

[scipio04]

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]]) : "

[Ram]

Show us your exact code please.

[scipio04]

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

[Ram]

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()).

[scipio04]

http://www.bioconductor.org/packages/release/bioc/vignettes/affy/inst/doc/affy.pdf

page 4

[Ram]

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

[scipio04]

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

[Ram]

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?

[scipio04]

i tried with example file from affy but still same error

[Ram]

That's weird. Maybe open a post on bioC support so the developer has a chance to look at what's going on?

https://support.bioconductor.org/new/post/?tag_val=affy

[scipio04]

ok i go take a look on it , thank you

[Kevin Blighe]

New post: https://support.bioconductor.org/p/9138838/

[benformatics]

I used tilingArray once to analyze some CEL files