Hi,

could you please suggest me why I am getting error with apeglm shrinkage in the code while the same code is working with normal shrinkage.

resultsNames(dds)
 [1] "Intercept"                          "group_Aman.Leaf.T2_vs_Aman.Leaf.T1"
 [3] "group_Aman.Leaf.T3_vs_Aman.Leaf.T1" "group_Aman.Root.T1_vs_Aman.Leaf.T1"
 [5] "group_Aman.Root.T2_vs_Aman.Leaf.T1" "group_Aman.Root.T3_vs_Aman.Leaf.T1"
 [7] "group_Boro.Leaf.T1_vs_Aman.Leaf.T1" "group_Boro.Leaf.T2_vs_Aman.Leaf.T1"
 [9] "group_Boro.Leaf.T3_vs_Aman.Leaf.T1" "group_Boro.Root.T1_vs_Aman.Leaf.T1"
[11] "group_Boro.Root.T2_vs_Aman.Leaf.T1" "group_Boro.Root.T3_vs_Aman.Leaf.T1"

resAmanRootT1vsAmanRootT2<-lfcShrink(dds,contrast=c("group","Aman.Root.T1","Aman.Root.T2"),type="normal") using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).

Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'. See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette. Reference: https://doi.org/10.1093/bioinformatics/bty895

summary(resAmanRootT1vsAmanRootT2)

out of 29097 with nonzero total read count adjusted p-value < 0.1 LFC
> 0 (up)       : 10, 0.034% LFC < 0 (down)     : 8, 0.027% outliers [1]       : 19, 0.065% low counts [2]     : 0, 0% (mean count < 0) [1] see 'cooksCutoff' argument of ?results [2] see 'independentFiltering' argument of ?results

resAmanRootT1vsAmanRootT2<-lfcShrink(dds,contrast=c("group","Aman.Root.T1","Aman.Root.T2"),type="apeglm")

Error in lfcShrink(dds, contrast = c("group", "Aman.Root.T1", "Aman.Root.T2"),  : 
  type='apeglm' shrinkage only for use with 'coef'

Thanks in advance for your time and help. nabiyogesh

Here's some documentation on the topic:

http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#extended-section-on-shrinkage-estimators