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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!

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  • $\begingroup$ What type of comparison? $\endgroup$ – arupgsh Aug 21 '17 at 17:11
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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.

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