I am analyzing microarray data for circadian experiments (8 timepoints, 4-hour sampling resolution) and I would like to do a COSOPT analysis. I could not find the COSOPT code or the email of Dr. Straume. Do you have acess to that code in a programming language? I wonder if someone can share the algorithm source. I already analyzed the data using JTK_Cycle. Do you know any other program for analyzing periodic patterns in genome-scale data sets?
The R package GeneCycle implements the robust Fisher-G test based on Wichert et al. (2004), Ahdesmaki et al. (2005) and Ahdesmaki et al. (2007) for detecting periodically expressed genes from gene expression time series data. it's particularly useful for handling missing data, and short time-series.
Also, Wijnen et al 2005 (Methods in Enzymology) suggest a different aproach using their F24 statistics. the paper in Methods provides the R script.
I do not think COSOPT is available, or in use much, anymore. As Eran suggests there is GeneCycle, there is also the R package JTK_CYCLE (Hughes et al., JBR 2010) and there is also Circwave (http://www.euclock.org/results/item/circ-wave.html).
Although often being used, conventional ANOVA is not suitable for time-series data, or for periodic analysis. It ignores the dependence between time points, and the circular nature of the data.
We implemented COSOPT ourselves and we are preparing to open the source codes written in C and R (but some bugs might be there). Please contact me if you still have an interest in using COSOPT.
Here is our published paper including source code of COSOPT. http://link.springer.com/article/10.1007/s10015-015-0237-6
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools