Hi there,

I am having issues with lfcShrink:

res <- lfcShrink (dds, contrast =c("zone", "transition", "peripheral"), res = w_res)

Error in lfcShrink(dds, contrast = c("zone", "transition", "peripheral"), : type='apeglm' shrinkage only for use with 'coef'

Please help.

When using lfcShrink() with type='apeglm', which is now the default method, you cannot specify a contrast. Instead, you have to set the value of the coef parameter, and its value must be one of the coefficients output by the following command:

resultsNames(dds)

If you want to use a contrast, then use the original shrinkage method by running:

res <- lfcShrink (dds, contrast =c("zone", "transition", "peripheral"), res = w_res, type = 'normal')

Kevin