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titaiwangms / anamiR

An integrated analysis R package of miRNA and mRNA profiiling
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multi_Differ does not produce any output! #1

Open Payamdel opened 6 years ago

Payamdel commented 6 years ago

Dear Wang, I tried to use function multi_Differ provided in R-package "anamiR" but the function does not generate any results!

library("anamiR")

Use the internal dataset

data("mirna", package = "anamiR", envir = environment()) data("pheno.mirna", package = "anamiR", envir = environment())

SummarizedExperiment class

require(SummarizedExperiment) mirna_se <- SummarizedExperiment( assays = SimpleList(counts=mirna), colData = pheno.mirna)

Finding differential miRNA from miRNA expression data with anova

multi_Differ(se = mirna_se, class = "Subtype", post_hoc = "scheffe.test")

No result is returned by the function!

Do you have any idea what the problem is? Best regards,

Payam

titaiwangms commented 6 years ago

Hi, @Payamdel

Thanks for replying. I am working on it. It seems like when I was focusing on the two main pipelines in anamiR, I forgot to update this function as well. Anyway, I will update it ASAP.

Many Thanks, Ti-Tai

Payamdel commented 6 years ago

Nice job! I can see that you have successfully updated the function! If I understood the code correctly, there is no option to correct for multiple hypothesis testing. Is it correct?

Moreover, the actual p-values are not reported in the result. Instead, True or False are presented. It would be informative to report the actual values.

titaiwangms commented 6 years ago

Hi, @Payamdel I am not sure if you are talking about post hoc test for anova. If it is, there are three methods you can choose, including "scheffe.test", "HSD.test", "duncan.test".

And that is really a great suggestion about showing P-value, appreciate that. I might update it later.