dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design= ~ batch + condition)
# dds <- estimateSizeFactors(dds)
dds <- DESeq(dds)
resultsNames(dds) # lists the coefficients
res <- results(dds, name="condition_trt_vs_untrt")
# or to shrink log fold changes association with condition:
res <- lfcShrink(dds, coef="condition_trt_vs_untrt", type="apeglm")

In the above code, if dds <- estimateSizeFactors(dds) is uncommented, I see the results are different. How does it affect the results? Thanks.

The message tells you what happens:

> dds <- makeExampleDESeqDataSet()
> dds <- estimateSizeFactors(dds, controlGenes=1:50)
> dds <- DESeq(dds)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

It uses the pre-existing sizeFactors(dds) however they were created (or simply assigned).