Question: differentially expressed genes
0
gravatar for pendyam.raveena
4.5 years ago by
pendyam.raveena10 wrote:

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 m trying it in R with limma package and facing many difficulties so pls can anybody help me out?

rna-seq R gene • 1.4k views
ADD COMMENTlink modified 4.5 years ago by wanghao.ecnu0 • written 4.5 years ago by pendyam.raveena10

its agilent.

 

ADD REPLYlink written 4.5 years ago by pendyam.raveena10

its asking me for cel files or gzipped ..m unable to do both.

ADD REPLYlink written 4.5 years ago by pendyam.raveena10
1
gravatar for Parham
4.5 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

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

ADD COMMENTlink written 4.5 years ago by Parham1.4k
1
gravatar for Zhilong Jia
4.5 years ago by
Zhilong Jia1.4k
London
Zhilong Jia1.4k wrote:

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

ADD COMMENTlink written 4.5 years ago by Zhilong Jia1.4k

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.

ADD REPLYlink written 4.5 years ago by Charles Warden6.9k
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