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

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.

rna-seq r next-gen
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updated by h.mon h.mon • written by williamsbrian5064 williamsbrian5064

1 answer

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)
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written by h.mon h.mon

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