Open sgosline opened 3 years ago
Related to #9, we want to evaluate the overall expression of all genes in the matrisome lists. To do this, we need to run the GSVA package.
1- download/install the GSVA tool: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7 https://www.bioconductor.org/packages/release/bioc/html/GSVA.html 2- convert the Matrisome gene sets to gene lists (the tool should tell you how) 3- assign each sample its own matrisome score based on the output of GSVA - this should be an x by y matrix where x is the number of matrisome lists and y is the number of samples 4- cluster the scores in a heatmap!
Related to #9, we want to evaluate the overall expression of all genes in the matrisome lists. To do this, we need to run the GSVA package.
1- download/install the GSVA tool: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7 https://www.bioconductor.org/packages/release/bioc/html/GSVA.html 2- convert the Matrisome gene sets to gene lists (the tool should tell you how) 3- assign each sample its own matrisome score based on the output of GSVA - this should be an x by y matrix where x is the number of matrisome lists and y is the number of samples 4- cluster the scores in a heatmap!