DESeq2: Multiple disease condition vs Normal
I have an mRNA dataset with one cell type and 3 different conditions (Metastatic, Primary Tumor, and Solid Tissue Normal).
I would like to compare the two diseased conditions with the normal. I am using the following code but getting the understated error.
deseq_res <- results(deseq_obj, contrast = list ( c('Primary Tumor', 'Metastatic'), c('Solid Tissue Normal')) , listValues=c(1, -1/3), alpha = 0.05, lfcThreshold = 1.5)
Error in checkContrast(contrast, resNames) :
all elements of the contrast as a list of length 2 should be elements of ‘resultsNames(object)’
I have checked if the names of the condition are identical to the ones in the dataset and they are. What can I do in this case?
Thanks in advance
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