<p>While trying to run the following code in <code>R</code>:</p>

<pre><code>list_of_sce &lt;- list()
# Looping though the UMI_count 'split_factor' columns at a time
split_factor = 500
for(i in seq(1,ncols, split_factor)) {
  num_loop = floor(i / split_factor) + 1
  idx = ncols
  if (i + split_factor &lt; ncols) {
    idx = i + split_factor
  } 
sce &lt;- SingleCellExperiment(list(counts=UMI_count[, i : idx]))
# Normalization of the dataset containing 
# heterogenous cell data (different cell types)
clusters &lt;- quickCluster(sce)
sce &lt;- computeSumFactors(sce, cluster=clusters)
list_of_sce[[num_loop]] &lt;- sce
}
</code></pre>

<p>I am getting the error:</p>

<pre><code>Error in .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  : 
cells should have non-zero library sizes
</code></pre>

<p>There are <code>warnings</code>, so when I run <code>warnings()</code> command I see the following:</p>

<pre><code>&gt; warnings()
Warning messages:
1: In .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  ... :
encountered negative size factor estimates
2: In .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  ... :
encountered negative size factor estimates
3:...
...
39:....
</code></pre>

<p>I do not understand why is this happening, and how to debug it. Any suggestions would be greatly appreciated.</p>

CC BY-SA 3.0
2017-12-19T07:45:22.423Z
What is the library size of the samples? computeSumFactors is failing because it can't compute the library size. I am not sure if your code is working as intended, shouldn't the `sce` be inside your loop?
llrs
CC BY-SA 3.0
2017-12-19T07:46:44.877Z
Do you have a sample with all 0s?
Devon Ryan
CC BY-SA 3.0
2017-12-19T08:16:10.020Z
Your code is different from another question you posted ([here](https://bioinformatics.stackexchange.com/q/3123/48)). Is this the same data/problem as in the linked question?
llrs
CC BY-SA 3.0
2017-12-19T15:17:03.777Z
It is the same. Where is the difference? Can't see it. These are related but different questions, so I asked them separately.
Nikita Vlasenko
<rna-seq><r><scran>
Error in .computeSumFactors: cells should have non-zero library sizes
# Error in .computeSumFactors: cells should have non-zero library sizes

(Asked by: username_0 on 2017-12-18)

While trying to run the following code in R:
list_of_sce <- list()
# Looping though the UMI_count 'split_factor' columns at a time
split_factor = 500
for(i in seq(1,ncols, split_factor)) {
  num_loop = floor(i / split_factor) + 1
  idx = ncols
  if (i + split_factor < ncols) {
    idx = i + split_factor
  } 
sce <- SingleCellExperiment(list(counts=UMI_count[, i : idx]))
# Normalization of the dataset containing 
# heterogenous cell data (different cell types)
clusters <- quickCluster(sce)
sce <- computeSumFactors(sce, cluster=clusters)
list_of_sce[[num_loop]] <- sce
}

I am getting the error:
Error in .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  : 
cells should have non-zero library sizes

There are warnings, so when I run warnings() command I see the following:
> warnings()
Warning messages:
1: In .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  ... :
encountered negative size factor estimates
2: In .computeSumFactors(assay(x, i = assay.type), subset.row = 
subset.row,  ... :
encountered negative size factor estimates
3:...
...
39:....

I do not understand why is this happening, and how to debug it. Any suggestions would be greatly appreciated.

**Tags:** rna-seq, r, scran
> **Comments:**
> **username_1**: What is the library size of the samples? computeSumFactors is failing because it can't compute the library size. I am not sure if your code is working as intended, shouldn't the `sce` be inside your loop?  
> **username_2**: Do you have a sample with all 0s?  
> **username_1**: Your code is different from another question you posted ([here](https://bioinformatics.stackexchange.com/q/3123/48)). Is this the same data/problem as in the linked question?  
> **username_0**: It is the same. Where is the difference? Can't see it. These are related but different questions, so I asked them separately.  

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## 0 answers

