kevin-haigis-lab / kras-allele-genetic-interactions Goto Github PK

The manuscript needs to be accompanied by "Source Data":

Please ensure that a Source Data file is included with your resubmission. Within the Source Data file, the relevant raw data from each figure or table (in the main manuscript and in the Supplementary Information) should be represented by a single sheet in an Excel document, or a single .txt file or other file type in a zipped folder. Uncropped blots and gel images should be pasted in and labelled with the relevant panel and identifying information such as the antibody used. An example of the Source Data file is available demonstrating the correct format:

https://www.nature.com/documents/ncomms-example-source-data.xlsx

The file should be labelled 'Source Data', with the title and a brief description included in your response here, and should be mentioned in all relevant figure legends using the template text below:

""Source data are provided as a Source Data file."""

In particular, please provide a source data file that contains the data behind your most important box plots and analyses e.g at least all of those in the main text.

I need to think carefully about the desired organization of the final product and then work backwards on how to be achieve this in the existing code base.

Below is a screenshot of their example XLSX file.

In the legend to the Supplementary Figures (e.g 1, 2, 3 and 10) please define the box plots e.g the quartiles/whiskers etc. Please state how many samples were analysed. While you note this in the legend to figure 4 this needs to be added to all figure legends, including figure 5. Each figure and its legend should stand alone.

• Add back the descriptions of the box-plots to all necessary figure legends.
• Check to make sure the number of samples is everywhere it needs to be.
• Also add back in the statements for Source Data.

Is not possible to provide the compiled data as a source data file? This can be a zip file.

• Zip the raw data and try to submit.

For getting it set-up: https://kevinushey-2020-rstudio-conf.netlify.app/slides.html#1

Hi,

This is a great work. Recently, I want to repeat the work in the paper, I found that some files are missing in the linker "https://figshare.com/articles/dataset/The_origins_and_genetic_interactions_of_KRAS_mutations_are_allele-_and_tissue-specific/14115569"

for example, the file cancer-data folder in the script "20_prepare-cancer-data.R". How can I find those files.

Best,

Wei

Below are several points of repetition that we want to reduce:

• Need not reference source data in each figure.
• Need not explain the box-plot demarcations in every figure with a box-plot.
• Change all secondary mentions of "Benjamini-Hochberg adjust p-values" to "FDR-adjusted p-values."

Secondary adjustments:

• Indicate that we have made these changes to reduce repetition in the response to the editor.

Below are a list of specific changes to figures that are required for the final submission of the manuscript.

Wherever statistics have been derived (e.g. error bars, box plots, statistical significance) the legend needs to provide and define the n number (i.e. the sample size used to derive statistics) as a precise value (not a range), using the wording “n=X biologically independent samples/animals/cells/independent experiments/n= X cells examined over Y independent experiments” etc. as applicable.

Please note that this information is missing in the legends of figures:

• Fig. 2b
• Fig. 4e
• Fig. 5a-d (lower panel)
• Supp. Fig. 1c
• Supp. Fig. 8b, d, f, h
• Supp. Fig. 10b

Please provide a precise value of ‘n’ in the legends of figures:

• Supp. Fig. 1b
• Supp. Fig. 2a-d
• Supp. Fig. 3a-d
• Supp. Fig. 6 (bar plots) - (no change to figure; add n = 1,199 biologically independent MM tumor samples to the legend)

Please note that the exact p value should be provided, when possible, in the legends of figures

• Fig. 2b
• Fig. 4e
• Supp. Fig. 2a-d
• Supp. Fig. 3a-d
• Supp. Fig. 10b

Please note that for the Fig. 4e and Supp. Fig. 10b, ***p-values and statistical tests are indicated in the legends. However, comparison for the same, "***" has not been represented in the figures. Please rectify this in the figures or legends as applicable. Also, if appropriate, please provide exact p-values.

• Fig. 4e
• Supp. Fig. 10b

The editor for our manuscript has requested that we create a DOI for this GitHub repository.

We strongly encourage you to make your code citable by obtaining a DOI for the Github repository. This can be done by linking the repository to Zenodo, following the instructions here: https://guides.github.com/activities/citable-code/. Please cite the Github repository in your manuscript text or Code Availability statement and in your reference list: authors, title (this paper), repository name, DOI identifier, year.

Add a sheet to the supplementary data with the results of the non-allele-specific comutation analysis. Make sure to also cite it in the text.

• make supplemental sheet
• compile Excel file and add names to sheets
• reference in text