<p>There seems to be some problem with your &quot;platform specific tempdir&quot; that is used by getGEO's <code>destdir</code> parameter. See <code>?getGEO</code> for more info on the <code>destdir</code> parameter.</p>
<p>Try</p>
<pre><code>GSE68808 &lt;- getGEO(&quot;GSE68808&quot;, destdir = getwd())
</code></pre>

CC BY-SA 4.0
2021-04-06T16:33:19.293Z
2021-04-06T16:33:19.293Z
Ram RS
<p>I've installed GEOquery with</p>
<pre class="lang-r prettyprint-override"><code>install.packages(&quot;BiocManager&quot;)
BiocManager::install(&quot;GEOquery&quot;)
library(GEOquery)
</code></pre>
<p>then I ran the command</p>
<pre class="lang-r prettyprint-override"><code>GSE68808 &lt;- getGEO(&quot;GSE68808&quot;)
</code></pre>
<p>but it resulted in..</p>
<pre class="lang-r prettyprint-override"><code>Found 1 file(s)
GSE68808_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68808/matrix/GSE68808_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4138819 bytes (3.9 MB)
downloaded 3.9 MB

error: 'C:\Users\(myname)\AppData\Local\Temp\RtmpUp5Sv7\file8e844a7a59bc' does not exist.
</code></pre>
<p>ㅜㅜ</p>
<p>How can I solve this? thanks.</p>

CC BY-SA 4.0
2023-09-15T20:22:32.093Z
Please consider accepting the answer if it has answered your question
M__
<geoquery><gse>
Error downloading GSE dataset
# Error downloading GSE dataset

(Asked by: username_0 on 2021-04-06)

I've installed GEOquery with
install.packages("BiocManager")
BiocManager::install("GEOquery")
library(GEOquery)

then I ran the command
GSE68808 <- getGEO("GSE68808")

but it resulted in..
Found 1 file(s)
GSE68808_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68808/matrix/GSE68808_series_matrix.txt.gz'
Content type 'application/x-gzip' length 4138819 bytes (3.9 MB)
downloaded 3.9 MB

error: 'C:\Users\(myname)\AppData\Local\Temp\RtmpUp5Sv7\file8e844a7a59bc' does not exist.

ㅜㅜ
How can I solve this? thanks.

**Tags:** geoquery, gse
> **Comments:**
> **username_1**: Please consider accepting the answer if it has answered your question  

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## 1 answers

### Answer by username_2 on 2021-04-06. Score: 0

There seems to be some problem with your "platform specific tempdir" that is used by getGEO's destdir parameter. See ?getGEO for more info on the destdir parameter.
Try
GSE68808 <- getGEO("GSE68808", destdir = getwd())


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