Open malbahrani opened 6 years ago
Hi @malbahrani, values are normalized using FPKM (NOT log2(FPKM+1) and they are not raw counts.
Hi, Is possible to have the raw count of CCLE transcripts?
Thanks.
Hi @BadSeby, Data for this project is available through codeocean. You can use this link (https://codeocean.com/2018/05/03/gene-isoforms-as-expression-based-biomarkers-predictive-of-drug-response-in-vitro-lsqb-pmid-colon-29066719-rsqb/code) to access the data, ccle data is available under data section (CCLE_hs.RData). To load and work with the dataset you need to install PharmacoGx package (http://bioconductor.org/packages/release/bioc/html/PharmacoGx.html). Let us know if you have any further question.
Best, Zhaleh
Hi @zhaleh-safikhani, I use RStudio and package PharmacoGx to open CCLE_hs.RData. I find the expression of isoforms in molecularProfiles->isoforms->essayData->exprs to recover isoforms expression (data are normalized in FPKM I believe). Since most popular tool for differential expression using raw count (DESeq, DESeq2, and EdgeR are not designed for differential expression analysis of isoforms. However, given the popularity of these methods, it might be tempting for an end user to identify DE isoforms using FPKM converted counts), It is possible have isoforms expression from CCLE_hs.RData in raw count without normalization step?
Hi, I am wondering, are the transcripts expression values in the
CCLE_hs.RData
file quantified in log2(FPKM+1)?There are values that seem more like count ...