I have three samples of RNAseq showing count values of gene expression which all of them are control conditions. Two of these samples are from same patient and the third sample is from another patient. I need to show the highly expressed genes within all the samples. To this end i used Deseq package like below:
dds <- DESeqDataSetFromMatrix(countData = cstm, colData = colData, design = ~ 1)
but the result shows the genes that are highly expressed in one sample which belonged to different patient in comparison to three samples. However I didn't enter the patients info in the coldata as I didn't want to be considered as a factor in this analysis. Does anyone a=has a better understanf=ding of how to show highly expressed genes within samples of similar conditions?