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!
Analyzing Illumina Counts
rna seq;normalization;illumina
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.