We are currently analyzing immune infiltration in samples obtained from mouse experiments and are interested to use seq-ImmuCC in our research.
In our case, we would like to have an idea of the absolute amount of immune fraction in each sample as well.
As the latest version of CIBERSORT is able to assess the absolute amount of immune cells, expressed in arbitrary units, we were wondering whether it would be a sensible approach to apply the RNA-seq preprocessing pipeline from seq-ImmuCC (RNASeq_pipeline.sh) first and apply the absolute mode of CIBERSORT with the "SignatureMatrix.rnaseq.csv" signature matrix afterwards.
Dear Dr. Chen
We are currently analyzing immune infiltration in samples obtained from mouse experiments and are interested to use seq-ImmuCC in our research. In our case, we would like to have an idea of the absolute amount of immune fraction in each sample as well.
As the latest version of CIBERSORT is able to assess the absolute amount of immune cells, expressed in arbitrary units, we were wondering whether it would be a sensible approach to apply the RNA-seq preprocessing pipeline from seq-ImmuCC (RNASeq_pipeline.sh) first and apply the absolute mode of CIBERSORT with the "SignatureMatrix.rnaseq.csv" signature matrix afterwards.
Kind regards Arne Claeys