federicomarini / ideal Goto Github PK

Dear federico,
The ideal application is really awesome. I am using it for an upcoming short practical course on rna-seq.

I'd like to have the annotation available for Arabidopsis. Yet, it is not pre-installed. I understand that this can be solved locally but could you have a look for the public instance of ideal?

This is my error message:
The package org.At.tair.db is not installed/available. Try installing it with BiocManager::install('org.At.tair.db').

In advance thank you
Marc

We talked about this one :)
https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files

Hello @federicomarini

Here is the problem I get when using the gene selected from the left menu.

This is the table from below and you can see that the Id column seems fine but that the table also has rownames (I guess).

On the left menu, I get this:

My guess is that the selection is based on the rownames of the table instead of the id column.

I'm trying to look for the bug myself but I'm having a hard time navigating the code since I'm not that used to shiny app code.

I think I'm trying to find where ths variable is instantiated:

EDIT: for context, I use gene_symbol as my main ID. I guess you use Ensembl ID by default and that is where this is problematic.

Hi everyone,

When trying to remove outliers from the "Optionnal step box". I get the following error :

Warning: Error in .validate_names: assay colnames() must be NULL or identical to colData rownames()

However everything works fine when constructing the dds object if i do not remove any sample...

Here is the code activated when clicking on the boxe's button :

observeEvent(input$button_outliersout, {
            withProgress({
                allsamples <- colnames(values$dds_obj)
                outliersamples <- input$selectoutliers
                keptsamples <- setdiff(allsamples, outliersamples)
                dds <- DESeqDataSetFromMatrix(countData = values$countmatrix[, 
                  keptsamples], colData = values$expdesign[keptsamples, 
                  ], design = design(values$dds_obj))
                dds <- estimateSizeFactors(dds)
                values$removedsamples <- input$selectoutliers
                curr_species <- input$speciesSelect
                values$dds_obj <- dds
                updateSelectInput(session, inputId = "speciesSelect", 
                  selected = curr_species)
                values$res_obj <- NULL
            }, message = "Removing selected samples from the current dataset")
        }) 

I do not understand why it's not working, colnames seem to be updated before the new DESeqDataSetFromMatrix function calling. Do you have any idea ?

Thanks you !

Elendill

Hi @federicomarini

I had this on the ideal_server GH - federicomarini/ideal_serveredition#11

Not sure if the error info should be posted here. Please advise.

Thanks in advance.

I find an intersection between the up and down regulated genes with Ideal.
("Intersection of gene sets" figure in the "Functional analysis" outlet). That is strange. Please find the figure in PJ
plot_vennlists.pdf

Best wishes,
Cala3len

Just to note that the annotation selection stage is giving an error at the moment, when selecting Zebrafish from the drop down for creating the annotation dataframe :

The package org.Dr.eg.db is not installed/available. Try installing it with BiocManager::install('org.Dr.eg.db')

Error: An error has occurred. Check your logs or contact the app author for clarification.
NULL