[miso-users] how to calculate fold change

[Maayan Kreitzman]

Hi Yarden,
In addition to the helpful relative expression values MISO produces, I 
want to get expression fold change for a given isoform. I've been doing 
it with the assigned reads.

In the line below, from the .miso_bf file, there are 3 isoforms (0, 1, 
and 2). But, I noticed that the first condition only has assigned reads 
for isoform 0 and 1, and not for 2 (the second condition has assigned 
reads for isoforms 0, 1, and 2). Is it ok to assume that any isoforms 
not listed have 0 assigned reads?

If using assigned reads isn't a good approach, what would you suggest?


thanks!


ENSG00000132938    0.62,0.25,0.13    0.33,0.03,0.00 0.90,0.56,0.44    
0.70,0.17,0.13    0.38,0.01,0.00 0.95,0.48,0.40    -0.08,0.07,0.00    
0.61,0.52,0.39 
'ENST00000431530.exon0_ENST00000431530.exon1_ENST00000431530.exon2_ENST00000431530.exon3_ENST00000431530.exon4_ENST00000431530.exon5_ENST00000431530.exon6_ENST00000431530.exon7_ENST00000431530.exon8_ENST00000431530.exon9_ENST00000431530.exon10_ENST00000431530.exon11_ENST00000431530.exon12_ENST00000431530.exon13','ENST00000380808.exon0_ENST00000380808.exon1_ENST00000380808.exon2_ENST00000380808.exon3_ENST00000380808.exon4_ENST00000380808.exon5_ENST00000380808.exon6_ENST00000380808.exon7_ENST00000380808.exon8','ENST00000542829.exon0_ENST00000542829.exon1_ENST00000542829.exon2_ENST00000542829.exon3_ENST00000542829.exon4_ENST00000542829.exon5_ENST00000542829.exon6_ENST00000542829.exon7' 
(0,0,0):37,(0,1,0):1,(1,0,0):11,(1,1,0):1    0:12,1:1 
(0,0,0):43,(1,0,0):16,(1,1,0):5,(1,1,1):2    0:20,1:1,2:2    13 +    
29598748,30002764,30002846    30077892,30077873,30077394

-- 
Maayan Kreitzman
Computional Biologist
Michael Smith Genome Sciences Centre
BC Cancer Agency
Vancouver, BC V5Z 4S6