text: user9709: I'm trying to plot a heat map for a "GSE133399", I retrieved the GSE using GEOquery package and then assigned to an object and then tried to plot a heatmap, but I was not successful, I used the following code in RStudio:
  install.packages("BiocManager")
  BiocManager::install("GEOquery")
  library(GEOquery)
  ## change my_id to be the dataset that you want.
  my_id <- "GSE133399"
  gse <- getGEO(my_id)
  length(gse)
  gse <- gse[[1]]
  gse
  pData(gse) ## print the sample information
  fData(gse) ## print the gene annotation
  exprs(gse) ## print the expression data
  
  ## exprs get the expression levels as a data frame and get the distribution
  summary(exprs(gse))
  exprs(gse) <- log2(exprs(gse))
  boxplot(exprs(gse),outline=FALSE)
  library(dplyr)
  sampleInfo <- pData(gse)
  sampleInfo
  ## source_name_ch1 and characteristics_ch1.1 seem to contain factors we might need for the analysis. Let's pick just those columns
  
  sampleInfo <- select(sampleInfo, source_name_ch1,characteristics_ch1.1)
  
  ## Optionally, rename to more convenient column names
  sampleInfo <- rename(sampleInfo,group = source_name_ch1, patient=characteristics_ch1.1)
  sampleInfo
  install.packages("pheatmap")
  library(pheatmap)
  ## argument use="c" stops an error if there are any missing data points
  
  corMatrix <- cor(exprs(gse),use="c")
  
  I get this error:
  Error in cor(exprs(gse), use = "c") : no complete element pairs
  
  I also  tried this:
  corMatrix <- cor(exprs(gse),use="c", use="complete.obs")
  
  I get this error:
  Error in cor(exprs(gse), use = "c", use = "complete.obs") : 
    formal argument "use" matched by multiple actual arguments
  
  I want to achieve this plot:
  
  
  user-1: The GSE133399 dataset contains both ATAC-seq and RNA-seq data, none of which can be queried with GEOquery which works only for microarray data.
  exprs(gse) ## print the expression data returns an empty object as you might have noticed, therefore the errors in the lines that follow this command.
  On the bottom of https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133399 at the Supplementary file section you can download FPKM-transformed count data and use these. I would be careful though as FPKM is not ideal for inter-sample comparison. I personally always (if feasable) download the raw data and then process myself, but for a guess on what is going on the FPKMs probably will do.
  
original_text: 9709: <p>I'm trying to plot a heat map for a &quot;GSE133399&quot;, I retrieved the GSE using GEOquery package and then assigned to an object and then tried to plot a heatmap, but I was not successful, I used the following code in RStudio:</p>
  <pre><code>install.packages(&quot;BiocManager&quot;)
  BiocManager::install(&quot;GEOquery&quot;)
  library(GEOquery)
  ## change my_id to be the dataset that you want.
  my_id &lt;- &quot;GSE133399&quot;
  gse &lt;- getGEO(my_id)
  length(gse)
  gse &lt;- gse[[1]]
  gse
  pData(gse) ## print the sample information
  fData(gse) ## print the gene annotation
  exprs(gse) ## print the expression data
  
  ## exprs get the expression levels as a data frame and get the distribution
  summary(exprs(gse))
  exprs(gse) &lt;- log2(exprs(gse))
  boxplot(exprs(gse),outline=FALSE)
  library(dplyr)
  sampleInfo &lt;- pData(gse)
  sampleInfo
  ## source_name_ch1 and characteristics_ch1.1 seem to contain factors we might need for the analysis. Let's pick just those columns
  
  sampleInfo &lt;- select(sampleInfo, source_name_ch1,characteristics_ch1.1)
  
  ## Optionally, rename to more convenient column names
  sampleInfo &lt;- rename(sampleInfo,group = source_name_ch1, patient=characteristics_ch1.1)
  sampleInfo
  install.packages(&quot;pheatmap&quot;)
  library(pheatmap)
  ## argument use=&quot;c&quot; stops an error if there are any missing data points
  
  corMatrix &lt;- cor(exprs(gse),use=&quot;c&quot;)
  </code></pre>
  <p>I get this error:</p>
  <pre><code>Error in cor(exprs(gse), use = &quot;c&quot;) : no complete element pairs
  </code></pre>
  <p>I also  tried this:</p>
  <pre><code>corMatrix &lt;- cor(exprs(gse),use=&quot;c&quot;, use=&quot;complete.obs&quot;)
  </code></pre>
  <p>I get this error:</p>
  <pre><code>Error in cor(exprs(gse), use = &quot;c&quot;, use = &quot;complete.obs&quot;) : 
    formal argument &quot;use&quot; matched by multiple actual arguments
  </code></pre>
  <p>I want to achieve this plot:</p>
  <p><a href="https://i.stack.imgur.com/Dk2eV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Dk2eV.png" alt="enter image description here" /></a></p>
   -1: <p>The GSE133399 dataset contains both ATAC-seq and RNA-seq data, none of which can be queried with GEOquery which works only for microarray data.</p>
  <p><code>exprs(gse) ## print the expression data</code> returns an empty object as you might have noticed, therefore the errors in the lines that follow this command.</p>
  <p>On the bottom of <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133399" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133399</a> at the <code>Supplementary file</code> section you can download FPKM-transformed count data and use these. I would be careful though as FPKM is not ideal for inter-sample comparison. I personally always (if feasable) download the raw data and then process myself, but for a guess on what is going on the FPKMs probably will do.</p>
  