Hi,

It could be quite a lot reasons since I am not aware of the input data format.

Did you follow the steps in our vignette? Or is there any warning/error information you can provide?

Perhaps you could firstly check if the gene identifiers or cell names are properly set? Then whether the data is well normalized to gain a non-zero minimum value?

And also check the integrated data matrix in the out put list, to see if the integration is done perfectly?

Best,
Weiyan

from landscent.

Thanks for your quickly reply.
Here is my code.
`
library(Seurat)
require(scater)
library(LandSCENT)
require(AnnotationDbi)
require(org.Hs.eg.db)
data(net17Jan16.m)

tumor info

tumor <- readRDS("./result/integration/seurat/seurat_integration1.rds")
tumor_sce <- as.SingleCellExperiment(tumor, assay = "RNA")

tumor_sce <- normalize(tumor_sce, log_exprs_offset = 1.1)
tumor.m <- as.matrix(assay(tumor_sce, i = "logcounts"))
min(tumor.m)
anno.v <- mapIds(org.Hs.eg.db, keys = rownames(tumor.m), keytype = "SYMBOL",
column = "ENTREZID", multiVals = "first")
unique_anno.v <- unique(anno.v)
tumor_New.m <- matrix(0, nrow = length(unique_anno.v), ncol = dim(tumor.m)[2])
for (i in seq_len(length(unique_anno.v))) {
tmp <- tumor.m[which(anno.v == unique_anno.v[i]) ,]
if (!is.null(dim(tmp))) {
tmp <- colSums(tmp) / dim(tmp)[1]
}
tumor_New.m[i ,] <- tumor_New.m[i ,] + tmp
}
rownames(tumor_New.m) <- unique_anno.v
colnames(tumor_New.m) <- colnames(tumor.m)
tumor_New.m <- tumor_New.m[-which(rownames(tumor_New.m) %in% NA) ,]
tumor_New2.m <- tumor_New.m
Integration.l <- DoIntegPPI(exp.m = tumor_New2.m, ppiA.m = net17Jan16.m)
str(Integration.l)
SR.o <- CompSRana(Integration.l, local = TRUE, mc.cores = 6)
`

from landscent.

Hi,

Thanks for providing your script.

But unfortunately, I do not spot anything wrong. This seems to be the standard procedure as I suggested in the vignette T_T

However could you tell me, in the 'Integration.l$expMC' matrix, how many genes are left?

Best,
Weiyan

from landscent.

`
dim(Integration.l$expMC)

10266 18489

`
10266 genes left

from landscent.

emmmmmm.....Seems also fine.

No idea what is going on here T_T

from landscent.