Weird results from DESeq
Hi everyone,
I have been using the StrandNGS software to analyze my RNA-seq data. For the quantification, previously I used to use RPKM normalization and the results looked OK. But last time I tried the DESeq normalization and got some weird results: in total ~30,000 genes were quantified and among them there were about 1,000 genes showed exactly same expression level. Those 1,000 genes were not relevant at all in terms of their type(protein-coding, miRNA, lncRNA, etc.) and their function. An example is like:
- Gene_name Expression_level
- Aaaa 0.56789
- Bbbb 0.56789
- Cccc 0.56789
- Dddd 0.56789
- Eeee 0.56789
......
Anyone has any idea why this is happening? Thanks a lot.
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DESeq doesn't perform quantification, so which values did you use as input? In addition, I hope this is about DESeq2?
This looks like the input (count data) is not imported to R properly. The possibility is that the numerical counts were read by R as characters.
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