I have a set of RNA-seq data, and i used cuffdiff,deseq2 and edgeR to do the normalization. However, the expression level of the housekeeping genes seems unstable during different time points,ie. have great fold-change.I am wondering if there is any solutions to normalize the expression matrix using a set of housekeeping gene row count as reference since they should express stably.Should i do the normalization work manually or there is some package i can use, or adjust the packages i mentioned before to make it work ?
The question becomes how stably expressed the house keeping genes actually are (they tend to be less stable than advertised). The simplest way to do what you mentioned is to subset the DESeqDataSet or DGElist by the house keeping genes, normalize that, and apply the resulting normalization factors back to the full dataset.