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drisso / zinbwave

Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave
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Error in zinbwave #63

Closed ZHIDIHUAYUAN closed 3 years ago

ZHIDIHUAYUAN commented 4 years ago

Hi, I have a problem in which I am trying to use the zinbwave package for differential expression analysis from scRNAseq data. My code is: cluster0_obwt_zinb <- zinbwave(cluster0_obwt_sum, K = 0, epsilon=1e12,observationalWeights=TRUE,BPPARAM=SerialParam()) Error in zinbInitialize(m, Y, nb.repeat = nb.repeat.initialize, BPPARAM = BPPARAM) : Gene 4 has only 0 counts! When I checked zero counts: t<-rowSums(assay(cluster0_obwt_sum)==0) summary(t) Min. 1st Qu. Median Mean 3rd Qu. Max. 0 1790 2337 2027 2487 2495 It shows that there is no genes that have only 0 counts.

yeroslaviz commented 4 years ago

It is difficult to see what you mean, when the message is not curated. Pls use the code option for your code.

Did you have a look at Gene 4?

From what I see you do have genes with rowSums ==0. The summary states the the min-value is 0, which imply that there are 0-values in the vector. Did you use some kind of filtering in your analysis?

e.g. (from the vigentte)

filter <- rowSums(assay(fluidigm)>5)>5