Is it possible to extract the baseMean data from each replicated sample using DESeq2? In DESeq, the output was arranged in a format of baseMeanA, baseMeanB, etc. that correlated with each sample. In DESeq2 so far I can only get a results output that has the baseMean calculated across all of the samples. I have replicated time points in a time course and would like the baseMean data for each time point as well as the overall baseMean.

Thank you.

We wrote the results table in DESeq2 to be more general, as sometimes users have dozens of conditions, or no replicated conditions but a crossed design, or numeric covariates, etc.

You can easily construct a table with the base means of each group using some custom code, for example, if the variable is 'condition':

baseMeanPerLvl <- sapply( levels(dds$condition), function(lvl) rowMeans( counts(dds,normalized=TRUE)[,dds$condition == lvl] ) )

Thank you for the very prompt and helpful response. The code above successfully gave me a table with the baseMeans for each time point. 

I would also like to get the baseMeans for each time point within each plant line. My data is 2 plant lines with multiple replicates per time point (6 time points total). In all, I would like a table with the baseMeans for all 12 different options with each mean being for a distinct time point and plant line. I am using the "time series experiment" online tutorial to scaffold my data entry. I tried to adjust the above program to fit my needs but was unable to do so; sorry I am extremely new with R.

Thanks

Thank you very much for your help.