Sample 3 has only 0 counts! #70
Description
Hello there and thank you in advance for your help!
I am running zinbwave on a single cell dataset with many 0s. The following is my code and error:
Cluster9 <- SingleCellExperiment(list(counts=GetAssayData(object = Aotus.Cluster9, slot = "counts")))
Cluster9
#class: SummarizedExperiment
#dim: 21456 119
#metadata(0):
#assays(1): counts
#rownames(21456): Aotus-ENSANAG00000002703 Aotus-LMNB1 ...
# Aotus-ENSANAG00000028075 Aotus-ENSANAG00000031036
#rowData names(0):
#colnames(119): ACGGAGATCTTCAACT-1_1 ACTGCTCCAATGGATA-1_1 ...
# GTCATTTCACAAGTAA-1_6 TCTTCGGGTCCGTGAC-1_6
#colData names(0):
# Filter lowly expressed genes, genes that do not have at least 1 reads in at least 1 samples
filter <- rowSums(assay(Cluster9)>1)>1
Cluster9 <- Cluster9[filter,]
# Identify the 100 most variable genes, which will be the input for zinbwave.
assay(Cluster9) %>% log1p %>% rowVars -> vars
names(vars) <- rownames(Cluster9)
vars <- sort(vars, decreasing = TRUE)
Cluster9 <- Cluster9[names(vars)[1:100],]
assayNames(Cluster9)[1] <- "counts" #To avoid needing to specify which assay we should use for the zinbwave workflow
# ZINB-WaVE
Cluster9_zinb <- zinbwave(Cluster9, K = 2, BPPARAM=SerialParam(), epsilon=1e12, normalizedValues=TRUE, observationalWeights = TRUE)
I get the following error:
Error in zinbInitialize(m, Y, nb.repeat = nb.repeat.initialize, BPPARAM = BPPARAM) :
Sample 3 has only 0 counts!
However, when I check the rowSums there doesn't appear to be any rows that return 0 counts.
table(rowSums(assay(Cluster9)) == 0)
#FALSE
# 100
Any suggestions/help would be much appreciated!
Best,
Amber