runPCA error - Githubissues

drieslab / Giotto

Spatial omics analysis toolbox

https://drieslab.github.io/Giotto_website/

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runPCA error #215

Open sailseem opened 2 years ago

sailseem commented 2 years ago

Dear developer,

I got an error when i run the PCA, it's really odd. test<-runPCA(gobject = pdac_test, expression_values = 'normalized',

scale_unit = T, center = F, method = 'factominer') Error in .local(x, ...) : argument "x" is missing, with no default

The previous steps look alright, I am using my data instead of sample data. Can you help me with it? Thanks

RubD commented 2 years ago

Hi, can you take a look at this link: https://rubd.github.io/Giotto_site/articles/github_issues.html and provide us with some more information? Did you try the example datasets and did that work? Is this a visium dataset or something else?

Can you check pdac_test@raw_expr and pdac_test@norm_expr ? Thanks

sailseem commented 2 years ago

Sorry, i did not try the example datasets, I am using my own dataset. pdac_test@raw_expr Error: no slot of name "raw_expr" for this object of class "giotto"

pdac_test@raw_exprs

pdac_test@norm_expr

RubD commented 2 years ago

Can you reproduce this error with one of the example datasets? It's hard figuring out what is happening here.