This is a test version of Biostars. For the public version, visit https://www.biostars.org.
differentially expressed genes

Hi all, how to convert text file to cel file? I have a dataset in text file format. My role is to find out differentially expressed genes, so I'm trying it in R with limma package and facing many difficulties so please can anybody help me out?

gene rna-seq r
• 2,988 views • link
updated by Ram Ram • written by pendyam.raveena • pendyam.raveena

It's asking me for cel files or gzipped .. I'm unable to do both.

• 0 views • link
updated by Ram Ram • written by pendyam.raveena • pendyam.raveena

2 answers

You need to install affypackage from bioconductor in R and then use it to import your data.

• 0 views • link
updated by Ram Ram • written by Parham Parham

For agilent, there is no cel format file. using limma directly. (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf)

• 0 views • link
updated by Ram Ram • written by Zhilong Jia Zhilong Jia

Yes - the .cel format is only for Affy arrays, and you can only go from a .cel file to a .txt file (not the other way around, because you lose information during the conversion). Also, some Agilent arrays are 2-color arrays, which would make no sense you tried to analyze them like an Affy array.

• 0 views • link
updated by Ram Ram • written by Charles Warden Charles Warden

Log in to answer this question.

More posts like this