I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated Fibroblasts (CAFs) cultured on DMEM, on DMEM + tumor from a patient named as 005 and DMEM + tumor from a patient named 036 something like this picture;
I want to know if NOF and CAF are different in terms of gene expression but I am not sure about design for DESeq2 or Edger and ANOVA.
By @Devon's help I have done so
> mycols cell_type co_cultured G2 NOF NO G3 NOF YES G4 CAF NO G5 CAF YES G6 CAF YES dds=DESeqDataSetFromMatrix(countData = NOFCAF,colData = mycols, design =~ cell_type*co_cultured)
Now, I am wondering what would be a suitable contrast for results function in DESeq2
> resultsNames(dds)  "Intercept" "cell_type_NOF_vs_CAF" "co_cultured_YES_vs_NO"  "cell_typeNOF.co_culturedYES" > res=results(dds) > res log2 fold change (MLE): cell typeNOF.co culturedYES Wald test p-value: cell typeNOF.co culturedYES DataFrame with 2545 rows and 6 columns
Thanks a lot for correcting me