Body: <p>I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again. </p>
  
  <p>I have .CEL files and I'm using the <em>Affy</em> package for R to read them. After I load all the files in, I then normalise the data and  generate a .txt file containing the expression values of each file (ranging from 11 to 12). Column 1 contains the gene names and the rest of the  columns contain the expression values for each of the files. </p>
  
  <p>I was wondering if there is a way to convert these data to bedgraph or BED format? What I'd like to do is a metagene analysis but I don't know how that would be possible with expression value data. </p>
  
  <p>I looked online and there are some kinda relevant suggestions/solutions, but they are for Windows machines and I'm working on MacOS.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-08T13:21:49.833Z
Comments.Text: Do the generated txt files contain the physical coordinates of the probes? If so, converting them to BED should be a simple matter of rearranging the columns (or they might already be valid BED files).
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-08T13:45:44.680Z
Comments.Text: Hi Konrad, thank you for your response.
  
  The generated txt file does not contain the coordinates of the probes, however, I have a gff file that contains all this information and I guess I could look up the coordinates for each gene of the array. However, I don't know how the expression values could be converted?
Comments.UserDisplayName: Min
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-08T14:58:08.140Z
Comments.Text: Why makes the solutions for Windows specific for Windows? Did you try to overcome these using equivalent programs or formats?
Comments.UserDisplayName: llrs
Tags: <r><microarray><format-conversion><chip-seq>
Title: How can I convert Affymetrix microarray data to bedgraph format?
ThreadText: # How can I convert Affymetrix microarray data to bedgraph format?
  
  (Asked by: username_0 on 2019-04-08)
  
  I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again.
  
  I have .CEL files and I'm using the *Affy* package for R to read them. After I load all the files in, I then normalise the data and generate a .txt file containing the expression values of each file (ranging from 11 to 12). Column 1 contains the gene names and the rest of the columns contain the expression values for each of the files.
  
  I was wondering if there is a way to convert these data to bedgraph or BED format? What I'd like to do is a metagene analysis but I don't know how that would be possible with expression value data.
  
  I looked online and there are some kinda relevant suggestions/solutions, but they are for Windows machines and I'm working on MacOS.
  
  **Tags:** r, microarray, format-conversion, chip-seq
  
  > **Comments:**
  > **username_1**: Do the generated txt files contain the physical coordinates of the probes? If so, converting them to BED should be a simple matter of rearranging the columns (or they might already be valid BED files).  
  > **username_0**: Hi username_1, thank you for your response.  The generated txt file does not contain the coordinates of the probes, however, I have a gff file that contains all this information and I guess I could look up the coordinates for each gene of the array. However, I don't know how the expression values could be converted?  
  > **username_2**: Why makes the solutions for Windows specific for Windows? Did you try to overcome these using equivalent programs or formats?  
  
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  ## 0 answers
  
  