titaiwangms / anamir Goto Github PK

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

I have a list of differentially expressed miRNA and mRNA and would like to use anamiR for further analysis. But I am not sure what values it takes as input for negative correlation function. I assume it is the normalized count. Is it true? If yes, could you please clarify, if we need to normalize the miRNA and mRNA data with the same normalized method? and how does it takes care of data coming from different methods (such as small RNA-Seq and RNAseq), is it comparable

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

I'm trying to install this package, but the Bioconductor told me that.

Hello, when I use the example code "table <- GSEA_ana(mrna_se = mrna_se, mirna_se = mirna_se, class = "ER", pathway_num = 2)", it shows error "Error in .local(drv, ...) : Failed to connect to database: Error: Can't connect to MySQL server on 'anamir.cgm.ntu.edu.tw' (110)", the function miR_converter also shows the same error.

what is the reason, and how to solve the problem?

Hello,
Looks like there is some server problem. "anamir.cgm.ntu.edu.tw" looks down and i can not connect to server. I hope it will fixed as sson as possible.

Best,
Samed

Hello,

I really like your package anamiR and its been a great help with my analyses. I wanted to ask if the versions of the databases used in the database_support() function is listed? I noticed that one of my miRNA-mRNA pairs had an experimentally verified interaction in miRTarBase v7.0, but it was not annotated in the output from the database_support(). Is there any way to select which versions of the databases to query?

Thanks,

Jenny