<p>The function you need is <code>CreateSeuratObject()</code> and not <code>Read10X()</code> as you start from TPMs.</p>

CC BY-SA 4.0
2021-05-21T13:44:08.397Z
2021-05-21T13:44:08.397Z
haci
<p>I have downloaded <code>log2(TPM/10+1)</code> values of <code>11,548 genes</code> and <code>9609 cells</code> from <code>GSE146026</code> (10x) in <code>tsv format</code> as the raw data is not available</p>
<p>I see patient IDs, cell barcodes, genes, even assigned clusters are here</p>
<pre><code>&gt; dput(head(a[1:5,1:5]))
structure(list(Cell_ID = c(&quot;10x_barcode&quot;, &quot;patient&quot;, &quot;time&quot;, 
&quot;sample_ID&quot;, &quot;clst&quot;), X10x_1 = c(&quot;10x_3288_t1_AAACATACCTTCCG-1&quot;, 
&quot;5&quot;, &quot;1&quot;, &quot;3288.1&quot;, &quot;1&quot;), X10x_2 = c(&quot;10x_3288_t1_AAACATACTCCTAT-1&quot;, 
&quot;5&quot;, &quot;1&quot;, &quot;3288.1&quot;, &quot;1&quot;), X10x_3 = c(&quot;10x_3288_t1_AAACATTGAACTGC-1&quot;, 
&quot;5&quot;, &quot;1&quot;, &quot;3288.1&quot;, &quot;1&quot;), X10x_4 = c(&quot;10x_3288_t1_AAACATTGCTGACA-1&quot;, 
&quot;5&quot;, &quot;1&quot;, &quot;3288.1&quot;, &quot;2&quot;)), row.names = c(NA, 5L), class = &quot;data.frame&quot;)
&gt;
</code></pre>
<p>I want to make a Seurat object of that but really I don't know how to do that</p>
<p>I have tried this</p>
<pre><code>    CreateSeuratObject(getwd(),gene.column = 2,cell.column = 1,unique.features = TRUE,strip.suffix = FALSE)
</code></pre>
<p>But get the following error:</p>
<pre><code>Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features) : 
  No cell names (colnames) names present in the input matrix
</code></pre>
<p>Anybody have ever dealt with such a case to help me please?</p>

<r><seurat><10x-genomics>
Making Seurat object from a processed file
# Making Seurat object from a processed file

(Asked by: username_0 on 2021-05-21)

I have downloaded log2(TPM/10+1) values of 11,548 genes and 9609 cells from GSE146026 (10x) in tsv format as the raw data is not available
I see patient IDs, cell barcodes, genes, even assigned clusters are here
> dput(head(a[1:5,1:5]))
structure(list(Cell_ID = c("10x_barcode", "patient", "time", 
"sample_ID", "clst"), X10x_1 = c("10x_3288_t1_AAACATACCTTCCG-1", 
"5", "1", "3288.1", "1"), X10x_2 = c("10x_3288_t1_AAACATACTCCTAT-1", 
"5", "1", "3288.1", "1"), X10x_3 = c("10x_3288_t1_AAACATTGAACTGC-1", 
"5", "1", "3288.1", "1"), X10x_4 = c("10x_3288_t1_AAACATTGCTGACA-1", 
"5", "1", "3288.1", "2")), row.names = c(NA, 5L), class = "data.frame")
>

I want to make a Seurat object of that but really I don't know how to do that
I have tried this
    CreateSeuratObject(getwd(),gene.column = 2,cell.column = 1,unique.features = TRUE,strip.suffix = FALSE)

But get the following error:
Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features) : 
  No cell names (colnames) names present in the input matrix

Anybody have ever dealt with such a case to help me please?

**Tags:** r, seurat, 10x-genomics

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## 1 answers

### Answer by username_1 on 2021-05-21. Score: 2 | Accepted answer

The function you need is `CreateSeuratObject()` and not `Read10X()` as you start from TPMs.


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