DESeq2 differential expression analysis

Class containing all elements generated during differential expression analysis with DESeq2. This class is essentially a list with validity checks to ensure DESeqTransform and DESeqResults correspond to the DESeqDataSet.

Value

DESeqAnalysis.

Slots

data: DESeqDataSet.
transform: DESeqTransform.
results: list. One or more unshrunken DESeqResults.
lfcShrink: list. Optional. One or more shrunken DESeqResults. If set, must correspond to those defined in results. Otherwise, can set as empty list (list()).

Note

Updated 2023-12-18.

DESeqDataSet

We recommend generating the DESeqDataSet by coercion from bcbioRNASeq object using as(dds, "bcbioRNASeq"). Don't use the DESeq2::DESeqDataSet() or DESeq2::DESeqDataSetFromMatrix() constructors to generate the DESeqDataSet object.

DESeqTransform

Object containing variance-stabilized counts. We recommend slotting the return from either DESeq2::varianceStabilizingTransformation() or DESeq2::rlog().

DESeqResults

Don't modify any of the DESeqResults objects manually. This includes rearranging the rows or dropping genes without adjusted P values. We'll take care of this automatically in supported methods.

Author

Michael Steinbaugh