What Kind Of Analysis And Visualization Methods Would One Use For Checking The Quality Of Rna Seq Count Data?

Question

[k.nirmalraman]

What kind of analysis and visualization methods would one use for checking the quality of RNA Seq count data...?

Basically looking for methods to detect sample contribution, replicates comparison, sample outliers.. etc! All I have to start with is Count Data... I have normalised it also using the DESeq method....

For visualization, I am looking for methods like MAplots, boxplots etc!! Suggestions and code snippets are very more welcomed

Thanks in advance

Answer 1

[epistatic]

I really like using R and the CummerRbund package makes it easy to work with cuffdiff output. If a similar database was made for Count data you may be able to use it. http://compbio.mit.edu/cummeRbund/