My R-Studio crashed and for some reason, I’m able to get most Wnt genes to plot their expression except for Wnt1 and Wnt10b, both of which are central to my poster. I brushed off the crash message thinking it was a regular one so I didn’t see what it said. I also created a brand new container but I still can’t get any expression out of the two genes and don’t get any plot results when I run stuff in the Console. Instead, I get graphs like the one below, which show no expression at all.
Ive had this happen to me multiple times for a gene I was interested in, MSTN,
This just means that there is absolutely no expression (or at least no perceived expression) of your gene in the MIXED GASTRULATION dataset.
If you would like to load the FULL DATASET try this code:
load(“~/workspace/c_moor_data/gastrulation/gastrulation_sce.rda”)
It may be because this is only the mixed gastrulation sample instead of the full dataset. If you plot the full dataset with all 139331 cells you should see some signals.
How do we switch the dataset we are working with again? Does it have to do with the
sce <- readRSD line?
I use this line to load the full dataset
load("~/workspace/c_moor_data/gastrulation/gastrulation_sce.rda")
I added the line but for whatever reason, I don’t have that file in my C_MOOR/c_moor_ccc_su22/ folder. I only have the one that ends in “.RDS”
Does this command work?
This file is not in the su22 folder. It is in the workspace/c_moor_data/gastrulation folder.
remember you will also need to run the sce <- logNormCounts(sce) command to log normalize the data before you can use it.
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Ah okay, that ended working, thank you very much!