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  • pauls
    Junior Member
    • Jun 2012
    • 1

    Can I use DESeq to analyse my data?

    Hi Simon and others,

    I was wondering if you could give me your opinion as to whether DESeq is suitable for analysing my data?

    Using an Illumina-based sequencing approach, I'm looking at the expression of an alternatively splicing gene in response to immune challenges. As such, the count data is not from RNA-seq, but from PCR gene product.

    Specifically, I'm looking at the counts of splice variants (rows; 12 variants for one exon, and 48 for another) in response to different treatments (columns), and at 2 different time points. I have only two biological replicates.

    Can I or should I use DESeq?

    Thank you!

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