4
$\begingroup$

I'm pretty new to all of this--forgive me if this is a simple question.

When I download illumina counts from GEO (like the supplementary file in GSE89225). Can I do comparisons directly on that file? Is there some normalization procedure I should go through?

Thanks!

Improve this question
$\endgroup$
1
  • $\begingroup$ What type of comparison? $\endgroup$
    – arup
    Aug 21, 2017 at 17:11

1 Answer 1

Reset to default
5
$\begingroup$

The counts files for GSE89225 is the output of HTSeq-count as a large matrix. Unless you are developing a differential expression package yourself you should not attempt to directly use this. Rather, you should load it into R and use packages such as DESeq2, edgeR, or limma (those are the most popular ones).

For convenience, in DESeq2 you would want the DESeqDatasetFromMatrix() function after loading this.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.