Final visualisation step about rasflow HOT 5 CLOSED

Hi, the error indicates that the problem happens when using the package mygene. It is used twice in scripts/visualize.R: line 57 gene.symbol.dea.all <- queryMany(gene.id.dea, scopes = 'ensembl.gene', fields = 'symbol') and line 106 gene.symbol.norm.table <- queryMany(gene.id.norm.table, scopes = 'ensembl.gene', fields = 'symbol')$symbol. As you said that volcanoplot is plotted (in line 88), so the error must come from line 106.

Reading the code in scripts/visualize.R from line 90 to line 106, it's clear that the problem is the normalized count table: control_gene_norm.tsv and treat_gene_norm.tsv. Could you check them out (maybe compare them with the example data data/example/dea/countGroup/oil_control_gene_norm.tsv and data/example/dea/countGroup/oil_low_gene_norm.tsv)?

from rasflow.

Hi,
I compared the files and found that there is an addition of the word gene: in front of the gene id if I remove all of these it runs. I will work on removing it in R, I could fix it easily in python, but if you have any suggestions on doing it in the script, that would be helpful. Thank you

from rasflow.

I see. The extra word "gene" before the gene ID confused the program. But the design of RASflow shouldn't add that extra word. So I can't figure out why that is happening without taking a look at your code and data. Otherwise, if a little bit of manual work (removing it manually) is OK for you, then it's fine.

from rasflow.

from rasflow.

Sounds great! I'll close the issue for now. Feel free to open it whenever it's necessary

from rasflow.