[prev in list] [next in list] [prev in thread] [next in thread] 

List:       bioconductor
Subject:    [BioC] Advise on analyzing NGS of many genes or intergenic peaks in
From:       "Xiaohui Wu" <wux3 () muohio ! edu>
Date:       2010-08-30 0:20:36
Message-ID: 201008292019506176921 () muohio ! edu
[Download RAW message or body]

Hi all,

I have NGS data (each tag is 20nt from 30 libraries, total about 60 million) in \
different conditions and have filtered some genes and intergenic regions (both called \
peak here, total about 20,000 peaks, rice). 

For now, I came up some ideas as follows:
1) the correlation of expression in these peaks (here expression is the normalized \
tag count) between each pair of libraries

2) cluster peaks or libraries based on their peak expression, like heatmap function \
in R

3) the fluctuation (or deviation) of each peak in these 30 libraries, to find what \
                peaks are with consistent expression and what peaks are with \
                fluctuated expression
    ** Is there any effective way to calculate something like this?  Is the standard \
deviation sd or coefficient of dispersion (sd/avg) enough?

4) DE peak between each pair of libraries or between each pair of clusters of libs. \
                Then use GO to compare the function of different sets of DE peaks.
    ** Here, I tend to use clusters of libs to reduce the times of comparison, but do \
you think I can treat the libs in the same cluster as different repliates then use DE \
package like EdgeR or DESeq to find DE peak?

5) relative peak usage among these libraries. 
    ** but I've no idea how to calculate this. I think just using (expression of the \
peak in one library) / (total expression of that peak in all libraries) is not \
suitable for this case, because there may some peaks expressed much lower than other \
peaks, while this won't be reflected in the formular.

Any idea is appreciated.

Thank you!

Regards, 
Xiaohui

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: \
http://news.gmane.org/gmane.science.biology.informatics.conductor


[prev in list] [next in list] [prev in thread] [next in thread]