Notebook 2 - KRAS cell line expression dataset

[gwaybio]

Thanks for making the analyses public @KwatME and @Kazyra - I am trying to reproduce the KRAS oncogenic signature output from notebook 2 (onco-gps-paper-analysis/notebooks/2 Generating Oncogenic Activation Signature.ipynb).

In part 2 (2. Read gene expression dataset) the line currently reads:

gene_exp = ccal.read_gct('../data/kras_isogenic_vs_imortalized.gct')

Should it be:

gene_exp = ccal.read_gct('../data/kras_isogenic_and_imortalized_celllines.gct')

I do not see the file '../data/kras_isogenic_vs_imortalized.gct' pre-loaded in the repo, nor instructions to download it in the download data notebook. I believe there are also 2 additional samples in the '../data/kras_isogenic_and_imortalized_celllines.gct' file.

If I am missing something critical, please let me know. Thanks!

[pablotamayo]

Kwat and Kate,

See below, this person trying to use the notebooks is having some trouble. Could you provide advise to this guy?

Let's keep track of issues like this so we can fix them and avoid future users from having the same problems.

Best,

--Pablo

---

Dr. Pablo Tamayo (ptamayo@ucsd.edu)

Group Leader, Computational Cancer Analysis Laboratory (CCAL) Co-Director, Cancer Center Genomics and Computational Biology Shared Resource Professor, Division of Medical Genetics, UC San Diego School of Medicine

UC San Diego Moores Cancer Center (Room 3017) 3855 Health Sciences Drive MC 0658, La Jolla, CA 92093-0658

Visiting Scientist, Cancer Program, Broad Institute of MIT/Harvard

---

On Wed, Sep 6, 2017 at 10:08 AM, Greg Way notifications@github.com wrote:

Thanks for making the analyses public @KwatME https://github.com/kwatme and @Kazyra https://github.com/kazyra - I am trying to reproduce the KRAS oncogenic signature output from notebook 2 (onco-gps-paper-analysis/notebooks/2 Generating Oncogenic Activation Signature.ipynb https://github.com/UCSD-CCAL/onco-gps-paper-analysis/blob/master/notebooks/2%20Generating%20Oncogenic%20Activation%20Signature.ipynb ).

In part 2 (2. Read gene expression dataset) the line currently reads:

gene_exp = ccal.read_gct('../data/kras_isogenic_vs_imortalized.gct')

Should it be:

gene_exp = ccal.read_gct('../data/kras_isogenic_and_imortalized_celllines.gct')

I do not see the file '../data/kras_isogenic_vs_imortalized.gct' pre-loaded in the repo, nor instructions to download it in the download data notebook. I believe there are also 2 additional samples in the '../data/kras_isogenic_and_imortalized_celllines.gct' file.

If I am missing something critical, please let me know. Thanks!

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[KwatMDPhD]

Hi @gwaygenomics,

Thank you for creating this issue. I've added the correct file in the /data directory. Sorry for forgetting about that file. Let us know if you have any other issues, comments, and/or questions.

Kwat

[gwaybio]

Thanks for the quick response @KwatME - I can confirm that its working now.

Best, Greg