search

neogilab / COVID19

Commands and codes used for the RNASeq and Proteomics data analysis SARS-Cov2 infected samples
1 stars 1 forks source link

Ask for help #1

Open millersan opened 4 years ago

millersan commented 4 years ago

Dear neogilab I have read the paper, the result is very interesting. Could you provide the Fractions data for me to test the result?
########### input <- "data/Proteomics/20200411_L1_Huh7_CoV_TMTPro_Fractions.csv" ########### Thanks a lot!

neogilab commented 4 years ago

The proteomics data can be downloaded from, https://zenodo.org/record/3754719#.XqgnSy2B3OQ

millersan commented 4 years ago

I tried this Rscript and I get this error,could you help me to solve this problem?

Rscript -e "rmarkdown::render('covid-19_proteom ics_preprocessing.Rmd')"

processing file: covid-19_proteomics_preprocessing.Rmd |.. | 2% ordinary text without R code

|... | 4% label: unnamed-chunk-1 |..... | 7% ordinary text without R code

|...... | 9% label: setup |........ | 11% ordinary text without R code

Quitting from lines 50-50 (covid-19_proteomics_preprocessing.Rmd) Error in setwd(dir) : cannot change working directory Calls: ... process_group.inline -> call_inline -> in_dir -> setwd

Execution halted

R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.6 (Maipo)

millersan commented 4 years ago

The proteomics data can be downloaded from, https://zenodo.org/record/3754719#.XqgnSy2B3OQ

I had download this data, but it seems like the raw data. Should I use the Thermo Scientific software to deal with them?

neogilab commented 4 years ago

Yes, you should use Proteome Discoverer to process the raw proteomics data. If you have further questions about the analysis pipeline, please feel free to contact us via official email. We are happy to help.