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SoupX: rowSums(data) : 'x' must be an array of at least two dimensions #294

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Urja25 opened this issue Aug 13, 2024 · 0 comments
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Urja25 commented Aug 13, 2024

A new issue seems to have arisen for me while executing SoupX during QC:

%%R -i data -i data_tod -i genes -i cells -i soupx_groups -o out
rownames(data) = genes
colnames(data) = cells
data <- as(data, "sparseMatrix")
data_tod <- as(data_tod, "sparseMatrix")
sc = SoupChannel(data_tod, data, calcSoupProfile = FALSE)
soupProf = data.frame(row.names = rownames(data), est = rowSums(data)/sum(data), counts = rowSums(data))
sc = setSoupProfile(sc, soupProf)
sc = setClusters(sc, soupx_groups)
sc = autoEstCont(sc, doPlot=FALSE)
out = adjustCounts(sc, roundToInt = TRUE)

I keep getting the error: Error in rowSums(data) : 'x' must be an array of at least two dimensions

This same piece of code worked for me on several occasions, but now the rowSums function does not seem to work. Can anyone help?

Thanks a lot in advance!

@Urja25 Urja25 added the bug Something isn't working label Aug 13, 2024
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