Swapping s1 with s3 would make the dendrogram result the same as the cufflink one, leaving the exact values away. But this does not look to be the case. Just checked the code again carefully. Also, tested the result with s1 and s3 swapped in DESeq, only got one significant gene. Plus, this gene is not in the 49 gene list that cufflink discovered. Also, this gene has 3 isoforms, none of them are in the 149 differential gene isoforms that cufflink output.
These convince me more that it was not I did anything wrong. I think this is because that HT-seq and cufflink assemble the counts differently. Not the problem of DESeq.
These convince me more that it was not I did anything wrong. I think this is because that HT-seq and cufflink assemble the counts differently. Not the problem of DESeq.
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