<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>

CC BY-SA 4.0
2019-04-08T13:21:49.833Z
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).
Konrad Rudolph
CC BY-SA 4.0
2019-04-08T13:45:44.680Z
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?
Min
CC BY-SA 4.0
2019-04-08T14:58:08.140Z
Why makes the solutions for Windows specific for Windows? Did you try to overcome these using equivalent programs or formats?
llrs
<r><microarray><format-conversion><chip-seq>
How can I convert Affymetrix microarray data to bedgraph format?
# 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 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?  
> **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

