Dear colleagues,

I'm trying to visualize my own RNA-seq data in the context of metabolic pathways. I first select "the metabolism_overview" under pathways, chose my mercator output containing bincode, name, identifier, description and type under mappings, and select my own experiment data (logFoldChange column). It gave me an error saying

"3302 out of 3753 data points have been sucessfully mapped to the bins of the choosen maping. However the pathway you choose does not show any of this bins. Either add those bins manually to this pathway or choose a different Pathway!"

But I don't have problem with the given examples and the bin numbers I got from mercator are all common pathway bin number and names. Does anybody have an idea what shall I do now? Really appreciate it!

Sun

Hi

what is weired is that you only have only 3753 datapoints for mRNA seq i would usually expect a couple 10k genes being detectable for a typical plant. Did you maybay filter your expression data?

Best Wishes
Björn