Hi I am trying to do a DESeq2 analysis. My PI previously batch corrected and vst transformed our gene expression data prior to sending it to me. I am trying to load it into a deseq data set but the code I am using it recognizing it as a count data set not a transformed data set. (i.e. when I try to run DESeq on my data set, it tells me it is not in integers, which is because it has been vst transformed). I believe the error is because the DESeqDataSetfromMatrix function input the gene expression data as count data. My question is what input method do I use instead to load the transformed matrix into a DESeq data set that keep it recognized as a transformed object?
Here is my full code up to the point of trying to create the DESeqDataSet
#Loading Geek Gene Expression data load("GEEK-ID 11576 genes outliers removed.RData") #Moving the file from a data frame to a matrix, we are also using the t() function to transform the matrix so it has participant numbers along the top and gene names along the side DESdata <- as.matrix(t(GEEKexpressionData)) # Now I will load the metadata (moved the file into the pasilla package extdata to make it so I didnt need to alter the code) pasAnno <- system.file("extdata", "Geek Data for DESeq2.csv", package="pasilla", mustWork=TRUE) coldata <- read.csv(pasAnno, row.names=1) #Now we will use the match function to make sure the rows of coldata match the columns of desdata keepers=match(rownames(coldata),colnames(DESdata)) #This created a vector that contained all the participant numbers in the coldate that had removed all races except caucasian and african american, and also removed CRP outliers newDESdata=DESdata[,keepers] #This now created a new matrix of the gene expression data, the participant columns have been made to match the rows of the coldata #There are NA columns present in the new matrix newDESdata that represent the that were previously outliers removed from the gene expression data #Next we will create a new matrix without these NA values newDESdata2 <- newDESdata[,colSumsis.na(newDESdata))