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bhklab / RNASeqDrug

Gene isoforms as expression-based biomarkers predictive of drug response in vitro
https://www.nature.com/articles/s41467-017-01153-8
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CCLE isoforms expression values #1

Open malbahrani opened 6 years ago

malbahrani commented 6 years ago

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 ...

zhaleh-safikhani commented 6 years ago

Hi @malbahrani, values are normalized using FPKM (NOT log2(FPKM+1) and they are not raw counts.

BadSeby commented 5 years ago

Hi, Is possible to have the raw count of CCLE transcripts?

Thanks.

zhaleh-safikhani commented 5 years ago

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

BadSeby commented 5 years ago

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?