Does Anyone understand the Sleuth Shiny app used to visualize your RNA-seq Data??

Question

[williamsbrian5064]

I was wondering if anyone knew how to interpret the Sleuth RNA-seq data? The column names are "pval", "qval", "rss", "sigma_sq", "tech_var", "mean_obs", "var_obs", "sigma_sq_pmax", "smooth_sigma_sq", and "final_sigma_sq". My goal with sleuth was to do a differential expression analysis but I can't figure this out? I feel like I'm missing something obvious here but I just don't have very much experience.

[GenoMax]

Have you looked at the getting started guide for sleuth?

Answer 1

[h.mon]

See this thread at the kallisto-sleuth users Google group. Quoting from that thread:

• target_id transcript name
• pval - pvalue
• qval - FDR adjusted pvalue using benjamini-hochberg
• b - the 'beta' value (analogous to fold change, though technically a bias estimator which has to do with the transformation)
• se_b - the standard error of beta
• mean_obs - the mean of the observations. this is used for the smoothing
• var_obs - the variance of the observations
• tech_var - the technical variance from the bootstraps
• sigma_sq - the raw estimator of the variance once the tech_var has been removed
• smooth_sigma_sq - the smooth regression fit for the shrinkage estimation
• final_sigma_sq - max(sigma_sq, smooth_sigma_sq). this is the one used for covariance estimation of beta (in addition to tech_var)