title: Why can't the pdf file created by gage (a R packge) be opened
body: <p>I am trying to use Gage package implemented in R to analyze my RNA-seq data. I followed the tutorial and got my data.kegg.p file and  I used the following script to generate the heatmap for the top gene set</p>
  
  <pre><code>for (gs in rownames(data.kegg.p$greater)[1]) {
    outname = gsub(" |:|/", "_", substr(gs, 10, 100))
    geneData(genes = kegg.gs[[gs]], exprs = essData, ref = 1,
    samp = 2, outname = outname, txt = T, heatmap = T,
    Colv = F, Rowv = F, dendrogram = "none", limit = 3, scatterplot = T)
    }
  </code></pre>
  
  <p>I did get a pdf file named "NOD-like_receptor_signaling_pathway.geneData.heatmap.pdf", but when I open this file with acrobat reader or photoshop, it gives the error information that this file has been disrupted and cannot be recovered. Could anyone help check this file (<a href="https://www.dropbox.com/s/wrsml6n1pbrztnm/NOD-like_receptor_signaling_pathway.geneData.heatmap.pdf?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/wrsml6n1pbrztnm/NOD-like_receptor_signaling_pathway.geneData.heatmap.pdf?dl=0</a>) to see whether it is really disrupted and is it possible to find a way to recover it? </p>
  
  <p>I also attached the R workspace file (<a href="https://www.dropbox.com/s/6n5m9x5hyk38ff1/A549.RData?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/6n5m9x5hyk38ff1/A549.RData?dl=0</a>). The object "a4" is the data with the format ready for gage analysis. It contains the data of the reference sample (nc) the treated sample (a549). It can be accepted by gage for analysis but generate the heatmap pdf file which cannot be opened (above). Would you mind helping me check whether these data can be properly used to generated the correct gage result?</p>
  
  <p>Best regards.</p>