Hello,
I have four conditions, two controls, and two experimental conditions. One of the proteins I am interested in analyzing was found to be absent in two of my control conditions but present in two of my experimental conditions in the LFQ intensity value.
But, after the differential enrichment analysis via DEP, the results table showed that the protein was downregulated (as opposed to induced/upregulated) in the experimental conditions. I followed the pipeline as provided in the document. I am wondering if there is some step I am missing and how to fix it. Please let me know if I can provide any further information to help.
Hello, I have four conditions, two controls, and two experimental conditions. One of the proteins I am interested in analyzing was found to be absent in two of my control conditions but present in two of my experimental conditions in the LFQ intensity value. But, after the differential enrichment analysis via DEP, the results table showed that the protein was downregulated (as opposed to induced/upregulated) in the experimental conditions. I followed the pipeline as provided in the document. I am wondering if there is some step I am missing and how to fix it. Please let me know if I can provide any further information to help.