Consult on data avalibility in your code

[wh960823]

Hello, we are using your software for our analysis. However, we found the datasets you used in genetic-map-construction.Rmd were not available now.
Could you please kindly provide us the data? That will be a great help for us.
Data links:
https://ucdavis.app.box.com/folder/49886630432
https://ucdavis.app.box.com/folder/498866304

Best,

[leejimmy93]

Hi, https://ucdavis.app.box.com/v/MaloofLab-Li-eQTL-2018 Can you try this? Let me know if it still doesn't work. Ruijuan

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On Sun, May 10, 2020 at 2:55 AM wh960823 ***@***.***> wrote: Hello, we are using your software for our analysis. However, we found the datasets you used in genetic-map-construction.Rmd were not available now. Could you please kindly provide us the data? That will be a great help for us. Data links: https://ucdavis.app.box.com/folder/49886630432 https://ucdavis.app.box.com/folder/498866304 Best, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADYWEXQZP5XBVCXMXXV3UY3RQZFXXANCNFSM4M5DX5DA> .

-- *Ruijuan Li* *Bioinformatics Scientist* *Cambridge, Boston* *PHONE: 334-332-9887INARI.COM <http://inari.com/>*

[wh960823]

Hi, Ruijuan
The link you provided works, thanks for your help.
I have another question in running the QTL-eQTL-mapping.Rmd using data you provided. The error was attached below

We are appreciate if you can help to solve the question.
Best,
Hao

[leejimmy93]

Hi, I don't think you attached any error message here.

[wh960823]

My mistake for missing an the error message, sorry.
The error message was as below

By the way, the input file used in this step can not be found. Could you please help me get accessible to the file batch_info.Rdata.

Best,
Hao

[leejimmy93]

I think you just need to change phenotype data to numeric, unfortunately the batch_info.Rdata is not available, but you can get the output from this step from the output folder on github "vstMat.f2.batch.corrected_revised.csv <https://github.com/MaloofLab/Li-eQTL-2018/blob/master/output/vstMat.f2.batch.corrected_revised.csv> ".

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On Wed, May 20, 2020 at 8:52 PM wh960823 ***@***.***> wrote: My mistake for missing an the error message, sorry. The error message was as below [image: TIM图片20200521084939] <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fuser-images.githubusercontent.com%2f42496682%2f82511536-2d649480-9b40-11ea-8678-d8c86732e9a6.png&c=E,1,gocswT7gPCAZsHs72dDbpwmy4sdJ9oqOY5T4De5gsM1Wgi5djAyoyh8o3SHXHvq0qDUc4d5ZEMcAwBhjwKgql6Eih0p-qbfdXyMc5B2e&typo=1> By the way, the input file used in this step can not be found. Could you please help me get accessible to the file batch_info.Rdata. [image: TIM图片20200521085108] <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fuser-images.githubusercontent.com%2f42496682%2f82511575-42412800-9b40-11ea-813d-c282c0e0b4e2.png&c=E,1,xt1PmuZ5_fCzFj3ouuM-D0EnJWrTEXgr2qukUQErOxHkSB_GXY_NpGMUFdNNWhsX-J3kv89V49TDoBk-yVlXjQpTk_NFL0-hKmB3Pcedt2j2ZyoJP_4,&typo=1> Best, Hao — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADYWEXXH43QLLO2IIGKRDCTRSR3MNANCNFSM4M5DX5DA> .

-- *Ruijuan Li* *Bioinformatics Scientist* *Cambridge, Boston* *PHONE: 334-332-9887INARI.COM <http://inari.com/>*

[wh960823]

Thanks for your reply. To be honest, I am not very familiar with R programming, so could you give me more details about how to change the phenotype data to numeric ？
Thanks