Hi, I've run DE on several bacterial libraries using DESeq and I've found that some genes are not expressed in either the treatment or the control, which means that a ratio is either 0 or cannot be calculated. The p-value, however is significant, which makes it tempting to assume that those particular genes are simply not expressed in any given situation. Am I correct?
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How can you calculate a p-value from no data? Bacteria are efficient; they don't keep much around that is never used. Possibly, the genes are used in situations that you have not tested... and possibly, it's an artifact of your experiment or analysis.
...and possibly, the expression level is below your detectable range.Last edited by Brian Bushnell; 10-06-2014, 01:58 PM. -
@sulfatereducers: Take a look at mbblack's posts in this thread: http://seqanswers.com/forums/showthread.php?t=45973Comment
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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