using ballgown, i have extracted expression values and sorted based on the pval of 0.05 and based on fold change classifying >1 as up and
Dear Karamveer
Let me know, these values are compared with any control?
If the values of these two variants of a gene are compared with a control sample or other counterpart of the experiment (for example with susceptible), then it could be considered as up-regulation as compared to control, and further, they are showing polymorphism within isoforms at their expression level. If you want to select the up-regulated gene, you can think about isoform giving the expression value 41.5.
All the best
Chet Ram
While you are comparing between the two contrasting samples and the resultant expression values you can roughly choose isofarm giving 41.5. While aligning your sample reads against the reference, you will get isofarm (genes), which you can again mark for SNPs on the map (for this gene' s neighborhood). If the SNP is assynonimous ( different alleles but for same amino acid) you can accept this value. Another computational approach for accuracy is Normalization of the value, which is proportional to mean length of given transcript under RPKM estimation.
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