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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Error in svd(x, nu = 0L, nv = 0L) : infinite or missing values in 'x' #119

Closed jungsoo0809 closed 3 years ago

jungsoo0809 commented 3 years ago

Hello, I'm trying to reveal reference cell type's spatial pattern on Visium samples following giotto's procedure like below.

[WIth 7 Visium samples]
 createGiottoVisiumObject -> normalizeGiotto -> calculateHVG -> runPCA -> createNearestNetwork -> doLeidenCluster

signature_matrix <- makeSignMatrixPAGE(sign_names = levels(factor(reference_data$Major_compartment)),
sign_list = reference_data_marker_lists)

my_giotto_object <- runSpatialDeconv(gobject = giotto, sign_matrix = signature_matrix)

But, I'm facing the error like on the title so I wonder what's the problem of it. Sorry for the naive question.

Thank you!

ndelrossi7 commented 3 years ago

Hi @jungsoo0809! runSpatialDeconv() requires a different kind of signature matrix. You can use the function makeSignMatrixDWLS() (recently updated on the suite branch). We are in the process of creating a tutorial for using DWLS deconvolution with Giotto which will be out soon! For more information on DWLS deconvolution in Giotto and what the expected input and output are, please check out this paper.

ndelrossi7 commented 3 years ago

Hi @jungsoo0809, just wanted to touch base to see if the issue was resolved! I have created some more in depth explanation of the different functions to create a DWLS signature matrix if that would be helpful.