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Dear Seqanswers community,
I am a newbie in the field of RNA-seq analysis and so, it might be a naive question for most of you.
I did Differential expression analysis amongst many samples with Cuffdiff2.0.4 . My model is a mouse model and I provided the gtf file from UCSC .
I am having hard time understanding how the FPKM values are calculated .
For eg,
I have an analysis between sample 1 vs sample 2
and between Sample 1 vs sample 3 . Should'nt the FPKM value for Sample 1 be the same in both the analysis?.
If not , Can you explain what is the fundamental logic behind the calculation of FPKM values and Differential expression.
Thank you all in advance for your help.
Himanshu
I am a newbie in the field of RNA-seq analysis and so, it might be a naive question for most of you.
I did Differential expression analysis amongst many samples with Cuffdiff2.0.4 . My model is a mouse model and I provided the gtf file from UCSC .
I am having hard time understanding how the FPKM values are calculated .
For eg,
I have an analysis between sample 1 vs sample 2
and between Sample 1 vs sample 3 . Should'nt the FPKM value for Sample 1 be the same in both the analysis?.
If not , Can you explain what is the fundamental logic behind the calculation of FPKM values and Differential expression.
Thank you all in advance for your help.
Himanshu
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