Excel table creating problem

[fengx90]

Deat ProTIGY team,

I have encountered an issue after analyzing the data that the excel table cannot be created and exported.
Do you have any solution/suggestion for this? It suggested that the Perl might be the problem, but I am sure I have Perl installed on the PC and I never had this problem before.
Thanks very much!

Best,
Feng

[nmclark2]

Hello Feng,

This issue seems very specific to your file and/or operating system as multiple members of our group have been exporting Excel files recently with no issues. Can you please provide some more details?

1. Your operating system and version
2. Your R version
3. The error printed in the R console (not the application) when attempting to export the Excel file.

Please note that many of us are currently on or starting our winter holiday soon, so we may not be as responsive.

Thank you,
Natalie

[nmclark2]

Hello Feng,

Has your issue been resolved? Please let me know if you are still experiencing issues. Otherwise, I will close the issue.

Thank you,
Natalie

[fengx90]

Dear Natalie,

Thanks a lot for the follow-up. It slipped my mind after holdiays. I am using Windows 10 system with R version 4.3.1 in RStudio. So my current solution is to get all info listed in the Excel file from the GCT file (I suppose they are the same). I can download the GCT file without any problem.

Here is what I got from the Shinny app:
Error msg: FALSE
If you are a Broadie and encounter this problem using Protigy on RStudio Connect please reach out to your administrator.
If you downloaded Protigy from GitHub and running it on your local computer, one possible reason could be that Perl is not installed on your computer.
For Windows OS you can install Strawberry Perl (http://strawberryperl.com/).
Please note that R needs to be restarted after installing Perl.)

The following was showed in R concole:
. No such file or directory\MASSSP1\AppData\Local\Temp\RtmpiCpzvo/WriteXLS/1.csv
The Perl script 'WriteXLSX.pl' failed to run successfully.
Saving file to C:/Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/Ma4w_Two-sample_mod_T_log2_2024-01-05-transformed-p-val_n1x9251.gct
Dimensions of matrix: [9251x1]
Setting precision to 4
Saved.
Saving file to C:/Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/Ma4w_Two-sample_mod_T_log2_2024-01-05_n8x9251.gct
Dimensions of matrix: [9251x8]
Setting precision to 4
Saved.
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/boxplots_unnormalized.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/correlation_boxplot.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/correlation_matrix_lo_spearman_up_pearson.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/experimentalDesign_Ma.txt (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/histogram_p-values.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/Ma4w_Two-sample_mod_T_log2_2024-01-05-transformed-p-val_n1x9251.gct (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/Ma4w_Two-sample_mod_T_log2_2024-01-05.xlsx (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/Ma4w_Two-sample_mod_T_log2_2024-01-05_n8x9251.gct (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/params.txt (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/pca.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/profile_plot.pdf (164 bytes security) (stored 0%)
adding: Users/MASSSP~1/AppData/Local/Temp/RtmpiCpzvoxyipr6459785650/volcano.pdf (164 bytes security) (stored 0%)

Thanks a lot!

Best,
Feng

[nmclark2]

Hello Feng,

Based on the error message, my best guess is there is something wrong with your Perl installation which does not allow the Excel file to save.

I would recommend performing a clean install of Perl on your machine, then try again.

Additionally, Protigy natively runs on R 3.6.1. It is possible that there is a version incompatibility issue with R 4.3.1. If the Perl re-installation does not work, I would recommend installing R 3.6.1 on your computer and running using that version.

Best,
Natalie

[fengx90]

Hello Natalie,

Thanks for the suggestion. I have tried both solutions, though I down-graded to R 4.1 instead of with R 3.6.1, in which I have used ProTIGY with no issues.

It keeps giving the error "The Perl script 'WriteXLSX.pl' failed to run successfully". I checked the Perl script and I cannot see anything usual (attached here). It would be so nice if you could cross-compare with the one on your PC. Or maybe you can send me a copy of it?

Best,
Feng
WriteXLSX.txt

[nmclark2]

Thanks for trying things out, Feng. As I've mentioned, we've had multiple users being able to use the Excel export. Also, you mentioned R 4.1 previously worked. The script you mentioned has not been changed in years. I have a suspicion that a change in machine, or the upgrade to Windows 10 might have caused this.

I am sorry I cannot be of more help right now. For now, you are correct that the GCT files contain the same information as the Excel file, so you can use these instead.

I will try and have someone with a Windows machine here test the script if time allows.

Best,
Natalie