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legumeinfo / ArachisPheno

AraPheno source code for http://arapheno.1001genomes.org
MIT License
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Peanut Core collection data into CSV format #1

Open sdash-github opened 4 years ago

sdash-github commented 4 years ago

Make a matrix format csv file from my summary spreadsheet of Roshan's trait data. Then, Sven can check its suitability for loading and other related issues.

sdash-github commented 4 years ago

ISSUE: Replicate data or Summary data (TODO Ask?)

AraPheno formats allow for loading data from replicates. Seems they encourage replicate data instead of just summary data per accession per trait. This being the background: -- Roshan's data has replicate data available along with average of replicates where available. -- Hence the question, which data should be loaded into ArachisPheno??

Ref to FAQ on replicates in AraPheno.

Ask:

SC, RK, EC, PO, ADF

sdash-github commented 4 years ago

Opinion for long term purpose: load replicate data.

adf-ncgr commented 4 years ago

agreed that loading replicates into ArachisPheno is the right thing to do. I think there are charts that allow users to see variability among these measures, for example.

piotyama commented 4 years ago

I agree too. I would want to have access to the raw data as a user rather than just averages.
@sdash-github, might I suggest you wait for a conference call we are scheduled to have with Greg and Noelle about this data? From Noelle's emails, it doesn't look like any of us have the complete dataset from FL 2013/2015 core phenotyping project.

sdash-github commented 4 years ago

Hi Sudhansu, I have another spreadsheet, manually curated phenotype data with replicate information (you might already have it). Let me know if you need that file, I can send it to you. Roshan

Great. I would have eventually looked or asked for it.

adf-ncgr commented 4 years ago

I agree too. I would want to have access to the raw data as a user rather than just averages. @sdash-github, might I suggest you wait for a conference call we are scheduled to have with Greg and Noelle about this data? From Noelle's emails, it doesn't look like any of us have the complete dataset from FL 2013/2015 core phenotyping project.

@piotyama thanks for the heads-up on this! we will likely just plow ahead in prototype mode with the data we have since we're trying to get the application into shape before funds expire. But, we won't invest too much in refining the data if as you say what we have now is only partial. thanks again

sdash-github commented 4 years ago

On 2020/3/28 11:47 AM, Roshan Kulkarni wrote:

Hi Sudhansu, phenotype_data_V1.xls contains the replicate data. Thanks, Roshan