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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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Error in scaleNotCenterFast(t(object@norm.data[[i]][object@var.genes, : Not an S4 object. #261

Closed Muchmorepig closed 2 years ago

Muchmorepig commented 2 years ago

when I analyzed my own data following: http://htmlpreview.github.io/?https://github.com/welch-lab/liger/blob/master/vignettes/Integrating_scRNA_and_scATAC_data.html

I met a problem: Error in scaleNotCenterFast(t(object@norm.data[[i]][object@var.genes, : Not an S4 object, when run scaleNotCenter(int_cim22d)

here is my code:

int_cim22d <- rliger::normalize(int_cim22d)

int_cim22d <- selectGenes(int_cim22d,
    datasets.use = 2,
    var.thresh = 0.05
    # combine = "intersection"
)

int_cim22d <- scaleNotCenter(int_cim22d)

packageVersion("rliger")                                                      
# [1] ‘1.0.0’
# R : 4.1

can anyone help me?

hummuscience commented 2 years ago

@Muchmorepig how did you solve this issue?