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Old 02-26-2015, 12:25 AM   #1
reuben.jacob
Junior Member
 
Location: Adelaide, Australia

Join Date: Aug 2014
Posts: 3
Smile NA entries in cummeRbund heatmap

Hi All,

I'm new to RNA-Seq and Bioinformatics. We have done a RNA-Seq study using Illumina Hi-Seq (paired-end, 90bp reads) on two cell types.

I have managed to remove the adapters, trim low quality reads and remove reads < 50bp (Trim Galore). I have then mapped them (TopHat-v2.0.8b) and assembled the mapped reads (Cufflinks). I then merged the reads (Cuffmerge) followed by differential gene analyses (CummeRbund).

When I generated a heatmap of the differentially expressed genes, I came across three instances of NA corresponding to a XLOC ID!

1) I'm not sure what this means?

2) Is there a way to remove these entries from the .db database and hence from the heatmap assuming that its something useless?

Any help would be greatly appreciated!

Cheers!
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cuffdiff, cummerbund, cummerbund plots, heatmap, rna seq

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