TCC-GUI suddenly closed

[RinaYona]

trafficstars

Hi,

After launching local TCC-GUI, I proceed to Exploratory Analysis (upload my data) and TCC Computation (Normalization Method; Deseq2, DEG Identification Method; Deseq2, FDR Cut off; 0.05), however the TCC-GUI suddenly closed and error was shown below R console. I can complete the analysis using the sample data, so I think my data form seems wrong. Could you give me any idea?

shiny::runApp(appDir = "TCC-GUI/")

Listening on http://127.0.0.1:5649 This Font Awesome icon ('clock-o') does not exist:

• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('clock-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('line-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('area-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-area' or 'fas fa-chart-area' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('cloud-upload') is deprecated in Font Awesome 5:
• please consider using 'cloud-upload-alt' or 'fas fa-cloud-upload-alt' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('area-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-area' or 'fas fa-chart-area' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('line-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('line-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('line-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('line-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages Warning in RColorBrewer::brewer.pal(N, "Set2") : minimal value for n is 3, returning requested palette with 3 different levels

Warning in RColorBrewer::brewer.pal(N, "Set2") : minimal value for n is 3, returning requested palette with 3 different levels

TCC::INFO: Calculating normalization factors using DEGES TCC::INFO: (iDEGES pipeline : tmm - [ edger - tmm ] X 3 ) Warning in estimateDisp.default(y = y$counts, design = design, group = group, : No residual df: setting dispersion to NA Warning: Error in glmFit.default: NA dispersions not allowed 1: shiny::runApp The name provided ('line-chart') is deprecated in Font Awesome 5:

• please consider using 'chart-line' or 'fas fa-chart-line' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('area-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-area' or 'fas fa-chart-area' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('bar-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-bar' or 'fas fa-chart-bar' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('file-pdf-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE

[swsoyee]

Thank you for using TCC-GUI. According to the screenshot, you don't have any replicate of each group. So the calculation will not perform well (sorry for the poor design of the error handing).

Also see: https://github.com/tgirke/systemPipeR/issues/4#issuecomment-316986983

Based on your design matrix and targets file, there are no replicates. Without replicates there is no sensible way to perform DEG analysis with most statistical methods.