Entering edit mode
Sole Acha, Xavi
▴
110
@sole-acha-xavi-4144
Last seen 10.3 years ago
Dear listers,
I have SOLiD Small-RNA Seq data for 250 samples, which are divided
into three sample types: 1 (n=50), 2 (n=100) and 3 (n=100). I have a
couple of doubts regarding how to proceed with the differential
expression analysis:
1) I want to compute differential expression analysis between each
pair of sample types (1 vs. 2, 1 vs. 3, 2 vs. 3). Do I need to
estimate the dispersions of each miRNA for each comparison (using only
the two sample types of interest in that comparison)? Or is it better
to estimate the dispersion only once using the three sample types
together and then compute the differential expression using this
overall dispersion?
2) When comparing types 2 vs. 3, I have a paired experimental design
(sample 1 from type 2 is the same as sample 1 from type 3). I would
like to use this information to get more power in my analysis. Is it
possible to perform a paired analysis with DESeq?
Thank you very much in advance for your help!
Best,
Xavi.
------
Xavier Solé Acha, PhD
Unitat de Biomarcadors i Susceptibilitat
Unit of Biomarkers and Susceptibility
Institut CatalĂ d'Oncologia // Catalan Institute of Oncology
Av. Gran Via de L'Hospitalet 199-203
08908 L'Hospitalet de Llobregat, Barcelona, Spain.
Phone: +34 93 260 71 22 / +34 93 260 71 86 (ext. 7122)
Fax: +34 93 260 71 88
E-mail: x.sole (at) iconcologia.net
[[alternative HTML version deleted]]