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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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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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