<p>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).</p>

<p>For convenience, in DESeq2 you would want the <code>DESeqDatasetFromMatrix()</code> function after loading this.</p>

CC BY-SA 3.0
2017-08-18T12:09:02.667Z
2017-08-18T12:09:02.667Z
Devon Ryan
<p>I'm pretty new to all of this--forgive me if this is a simple question.</p>

<p>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?</p>

<p>Thanks!</p>

CC BY-SA 3.0
2017-08-21T17:11:48.763Z
What type of comparison?
arup
<rna-seq><normalization><illumina>
Analyzing Illumina Counts
# Analyzing Illumina Counts

(Asked by: username_0 on 2017-08-18)

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!

**Tags:** rna-seq, normalization, illumina
> **Comments:**
> **username_1**: What type of comparison?  

---

## 1 answers

### Answer by username_2 on 2017-08-18. Score: 5 | Accepted answer

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.


---

