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UMMS-Biocore / debrowser

Differential Count Data Analysis Toolbox
GNU General Public License v3.0
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Error in DESeqDataSet: counts matrix should be numeric, currently it has mode: logical #201

Open nirbuj opened 5 years ago

nirbuj commented 5 years ago

Hi, the browser looks great but im unable to do a DE analysis getting this error all the time and terminal closes. my count table is similar to the example (first column gene names, first row sample names )

any thoughts?

Thanks in advance

debrowser files nir.zip

nephantes commented 5 years ago

I checked your files. They are all good. You shouldn't get any error. Which DEBrowser version are you using? You can also try https://debrowser.umassmed.edu as well to test. The latest version is installed there. Since, your files are comma separated, make sure to select "Comma" as separator while uploading. Let me know, how it goes.

nirbuj commented 5 years ago

Thanks for the quick replay. Im using DEBrowser 1.10.6 unable to open https://debrowser.umassmed.edu probably because of institutional IP restrictions of my university ): when i do a DE analysis on just the samples it works ok. but when i try to do meta on treatment cond1/cond2 dont show sample names and i cant choose either. selecting run gives the above error

nephantes commented 5 years ago

I got it. If you want to use your meta data in the condition selection, you cannot define more than two conditions in a column, since you compare 2 conditions. What you can do is you can define multiple columns and only keep 2 conditions in each column and keep the rest of the cells empty. In this way you can add as many comparisons as you want in the condition selection page.

nirbuj commented 5 years ago

your right, works great!!! amazing visual options!

nephantes commented 5 years ago

I improved error reporting while choosing the conditions from metadata. If there are more than 2 conditions, it warns about it.

nirbuj commented 5 years ago

really nice!! is there a way for plots to show the type of condition i wrote in the metadata file?(example treatment: cond1 = Ova , cond2 = control) i dont see a heatmap but i do have its settings options? thanks again for your help and creating this tool

nephantes commented 5 years ago

Is this something you are looking for? You can change the naming yourself, since those values are normalized log10, we gave this option to the user that they can give any name they want.

screen shot 2019-01-28 at 9 38 46 am