Question: Help with statistical parameters in ANOVA for gene expression
gravatar for luciano.anselmino
3.7 years ago by
luciano.anselmino0 wrote:

Hello everyone, I'm new in bioinfomatics analysis. I am analyzing datasets that I download from the GEO database, my goal is to identify genes that are differentially expressed in cancer patients undergoing different treatments, using normal tissue expression data as controls. I am using the Exatlas tool to perform this analysis. I have many doubts about the statistical parameters that I should use, especially when performing the ANOVA. I would like to know if any of you can give me a general screen about what the following terms mean and that thresholds and error models recommend using it to make this analysis reliable. Thank you so much.

ANOVA Parameters:

  1. Cutoff (probes with maximum value below cutoff are ignored)
  2. Threshold z-value used to remove outliers (0 - 1000)
  3. Proportion of probes with high error variances to ignore in error models (0 - 0.5)
  4. Bayesian degrees of freedom (used with error models 3 or 5) (4 - 1000) 5.Error model number (see the list below)

List of error models 1 = Actual error variance for each probe 2 = Average error variance for probes with similar expression level 3 = Bayesian correction of error variance (Baldi & Long 2001) 4 = Maximum between actual and expected average error variances 5 = Maximum between actual and Bayesian error variances

rna-seq gene expression gene • 1.0k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 3.7 years ago by luciano.anselmino0
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