Dear All,
I run DESeq2 of liver transcriptomic. I prefiltered my dataset to contain at least 4 raw count and at least 3 biological replicates to be included in the analysis, leaving 14,332 genes in the dataset and I would like to analyze for DEG to compare the two group with 8 biological replicates. I run a standard DESeq2 analysis in R and found >6000 "NA" values in the Padj. When I checked the genes with "NA" padj, many of those actually have between 50-100 raw counts without zero count within the group, which make the "NA" output does not make sense when we have non-low count reads of those genes. I know there is normalization process but the normalized values of those genes with "NA" padj are also not low. Any advice is greatly appreciated.
Best regards, Agung
include your problematic code here with any corresponding output
please also include the results of running the following in an R session
sessionInfo( )
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