I have used DESeq2 to analyse some RNAseq data and am using regularized log transformed data (rlog) output from DESeq2 to plot heatmaps.
However I am struggling to understand how the rlog output relates to the actual number of reads obtained for that gene. Can anyone explain this to me? For example, if I have a regularized log value of -1 for a particular gene, does this mean that I had less than 1 read for that particular gene in my sample (if so, how can this be)?
The reason I would like to understand this is I want to set a threshold for gene expression, so I am only looking at well expressed genes in my analysis. Is this possible with regularized log transformed data? Or would it be better to use a metric like RPKM? I was under the impression that working with regularized log transformed data is more advisable than RPKM, but perhaps in this instance RPKM is more appropriate.
Many thanks in advance for your help, Amy