Error in running IntegrateData()

[JieWu2012]

Hi,

When I run , I got error:

>mm.combined <- IntegrateData(anchorset = mm.anchors)
Merging dataset 11 into 10
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 1 into 3
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 4 into 3 1
Extracting anchors for merged samples
Finding integration vectors
Warning: Different cells in new layer data than already exists for scale.data
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 2 into 6
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 5 into 6 2
Extracting anchors for merged samples
Finding integration vectors
Warning: Different cells in new layer data than already exists for scale.data
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 8 into 6 2 5
Extracting anchors for merged samples
Finding integration vectors
Warning: Different cells in new layer data than already exists for scale.data
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 3 1 4 into 10 11
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Warning: Layer counts isn't present in the assay object; returning NULL
Merging dataset 7 into 9
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
Error in FindWeights(object = merged.obj, integration.name = integration.name,  : 
  Number of anchor cells is less than k.weight. Consider lowering k.weight to less than 66 or increase k.anchor.

I tried to set k.weight to NA, stll report error:

> mm.combined <- IntegrateData(anchorset = mm.anchors, k.weight = NA)
Merging dataset 11 into 10
Extracting anchors for merged samples
Error in if (nrow(x = filtered.anchors) < k.weight) { : 
  missing value where TRUE/FALSE needed

If I set k.weight to 65. It works without any error.

My question is: is it correct to set it to 65? What about other numbers less than 66? How should I set this number?

Thx

[longmanz]

Hi,

Is it possible that one of your dataset has number_cells less than 66? In that case you will need to set this number to a smaller one to avoid this. We will close it for now and please feel free to re-open it if the issue persists.