Which bioconductor package is ideal for performing ANOVA statistical filtering for an expression profile?

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

How to manually calculate p value in ANOVA? what is the equation or formula for it?

03 March 2021 4,928 5 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Mixed ANOVA - help?

I'm currently working on a piece which asks to conduct an ANOVA - looking at the effect of sporting group (2 levels), and exercise trials (two trials with six levels). I've computed this all...

27 February 2021 9,626 4 View

How to Interpret Partial Eta Squared Numbers For a Repeated Measures Anova?

I have obtained Partial Eta Squared Numbers through Two-Way Mixed Anova Analysis. My results for different constructs are: .105, .135, .038, .068, .061 respectively. I wanted to know, whether...

24 February 2021 7,122 1 View

Can we proceed to perform Two-way Mixed-ANOVA despite normality violations?

While testing assumptions, Shapiro-Wilk Test failed. However, I proceeded with the analysis and the interaction effect was significant. During our course- lectures, it was mentioned that Anova...

24 February 2021 228 3 View

Sample size determination for non-parametric tests?

How do I run a a priori sample size determination for non-parametric tests, like the Mann-Whitney U-test and the Kruskall-Wallis or other non-parametric tests that accord with the unpaired t-test...

24 February 2021 166 6 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Could you please suggests a tutorial or paper or any other materials to learn multiple gene expression in TCGA and GTEx databases?

I would like to analyze multiple gene expressions in normal and cancer tissue by using the data in the TCGA and GTEx databases. Please suggest a tutorial or paper showing step by step analysis of...

23 February 2021 9,007 3 View

Three-way robust ANOVA in R?

I am trying to conduct a three-way robust ANOVA in R using the WRS2 package as: t3way(Stem ~ Species*Temperature*Salinity, data = tutto) and there is an error saying : Error in if...

22 February 2021 1,674 8 View

Noha A. Mostafa

check this:

https://www.bioconductor.org/packages/devel/bioc/manuals/genefilter/man/genefilter.pdf

I hope you will find it useful

Austin Nguyen

Thank you Noha for your prompt response. It was not quite what I was looking for (as I already know how to use some of testing tools) but I was looking for a package that could take data directly from the GSEmatrix and directly analyze that. Thank you