Omics Playground

[Shahab email 14.3.3023] The older version had two options for generating heatmaps while the new one

[Shahab, email 13.3.2023] the older version had two options for generating heatmaps while the new one

resolved. On Friday, 10 March 2023 at 01:00:27 UTC+1 BigOmics Analytics Team wrote: submitted issue

Hi Daniel, Celltype estimation/deconvolution is indeed one of the strong functionalities in

Hi Marian, You're hitting the right questions and answers. It seems your experiments need batch

Thank you for your email! There is no method of choice for batch correction, our approach is to

At the moment not directly. You would need to extract the count matrix and metadata (sample

Hey there. Still having problem with this? On Wednesday, December 21, 2022 at 11:54:59 PM UTC+1

I am currently working on TMT proteomics analysis. The software does not (to my knowledge!) handle

Hi! Thank you for a very slick software. It takes some time to really learn but fantastic after that.

Figured this one out. FDR sets the threshold for what q-level each individual test needs to be to

In one of our projects, we have 4 columns defined in samples.csv, and one of these is a binary

For proteomics data, I would recommend running T-tests for DE analysis and the Fisher test for GSEA.

Hi, I've found some interesting subgroups in the clustered heatmap view, and would like to get

Hi. For the unsupervised methods, like the heatmap, you are not allowed to explicitly use any of the

Thanks again for your help. I will wait patiently for your input on how the beta features work. Best

I am getting disconnected running a list with ~100 DEPs on a local docker. anyone knows a workaround

Doubt would be a strong word. I have been working with proteomics data analysis for some year now,

Hi Wilson. I guess this question is best to ask in a forum for scRNAseq, like Seurat. Frequently in

Hello! Your correct on all points. Many people have used the Playground successfully for proteomics

Hi Sara. First, please try to pull the newest docker. We recently fixed a bug. If you still get

Hi Vikram. BigOmics Playground need your original raw data (counts, intensities). Your file contains

There are different ways you can do it 1. Merging the data sets, then assess for batch effects and if

Best is the raw counts (if you have) if you use edgeR and DEseq2 algorithms. If you supply normalised

Hey guys, I think I observed an issue with the heatmap rendering function. In the left dendogram, I

Hi Thorben. It's confusing because (I think) there are two types of "multiple testing"

Hi Matthias. I checked the latest docker image, and the CSV fiiles from the example.zip file should

Hi Eduardo. Are you using the docker version or one of our public servers (public.bigomics.ch or

We use the Spearman's rank correlation for the calculation which is calculated as the Pearsons

Great question. In Omics Playground, the multiple test correction is done before q-value aggregation.