Convert CEL to TXT

Understanding CEL and TXT file formats

CEL files are primarily associated with Affymetrix, a company that produces microarray technology. These files store the results of gene expression experiments and contain raw data from the microarray scanner. They are used in bioinformatics for analyzing gene expression levels.

TXT files, on the other hand, are plain text files that contain unformatted text. They are widely used for storing data in a simple, human-readable format and can be opened by virtually any text editor.

Why convert CEL to TXT?

Converting CEL files to TXT format can be beneficial for researchers who need to analyze or share data in a more accessible format. TXT files are easier to manipulate and can be imported into various data analysis tools and software.

Best software for CEL to TXT conversion

One of the best tools for converting CEL files to TXT is Affymetrix Power Tools (APT). This software suite provides a command-line interface for processing and analyzing microarray data. It includes utilities for converting CEL files to TXT format.

To convert using APT, you can use the following command:

apt-cel-to-txt -i input.cel -o output.txt

Another option is to use R with the affy package. This package allows you to read CEL files and export the data to a TXT file. Here’s a basic example:

library(affy)
celData <- ReadAffy(filenames="input.cel")
write.table(exprs(celData), file="output.txt", sep="\t")

Steps to convert CEL to TXT using R

1. Install the affy package in R.
2. Load the package using library(affy).
3. Read the CEL file using ReadAffy().
4. Export the data to a TXT file using write.table().

Conclusion

Converting CEL files to TXT format is a straightforward process with the right tools. Whether you choose Affymetrix Power Tools or R, both methods provide efficient ways to handle and analyze your microarray data.