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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!
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!