Entering edit mode
7.4 years ago
1769mkc
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1.2k
Can I use normal statistical test on cufflink data since its already normalised , so can i use parametric statistics on those normalised data and find differential expression , instead of running doing a cuff-diff analysis ?
Any suggestion would be highly appreciated
well i already did the tophat protocol but Im looking to test differential expression apart from cuffdiff , like can i apply T- test on the cufflink nopmralised data ?
FPKM/RPKMs are not directly comparable between samples. See this video of Lior Pachter https://youtu.be/5NiFibnbE8o?t=1833
In general to get interpretable and trustworthy results, it is almost always better to use generally accepted piece of software. In this case you also can have feedback from community. For your case, have a look here http://bioconductor.org/packages/release/bioc/html/tximport.html