tbaccata / amica Goto Github PK

Hi, I would like to use Amica for my proteomic data.
However, when I uploaded my files, the screen changed to grey and does not move from there.
So, I tried to run Amica from R and there was an error message like below.

Warning: Error in $<-.data.frame: replacement has 0 rows, data has 48

Could you tell me what I did wrong?

Kind regards,
J.

Hi,
I am trying to analyze MaxQuant data on local installation of amica. But when I upload the proteinGroups.txt file, a message appears stating that the maximum upload size exceeded, how can I solve this issue?

Regards,
Bola

Dear Sebastian and amica team,
Thanks again for all your work to make this useful tool publicly available.
I understand that the imputation is necessary for some of the features in amica, however this may affect the analysis for some of the proteomics data. This includes the analysis of the IP samples, where the bait protein and some potential binders are only present in one group. Or the proteomic analysis of the samples with the knockout genes. Is there any options in amica to count for these cases?
Can we have a new feature to generate new plots (maybe Venn?) for the samples before imputation?
Thanks

Hello,
Thank you for developing this tool. I am using FragPipe output. I used to be able to use it but now I am stuck on a faded grey page after clicking on Analyze both on the web version and the R version. On the R version, in the terminal, this error is displayed Warning: Error in [[: attempt to select less than one element in get1index 1: runApp
Could you help please ?
Thank you in advance for your help.

Input file firsttwolines.txt
Contrast file contrast.txt
Design file design.txt

Hi, everything works nicely for me and I find amica outstanding, only thing I can't produce is heatmaps. For some reason I get this error "Not all levels of the column_side_colors are mapped in the column_side_palette. Could you help with this?
Thanks a lot!

Hello,

I encountered an error when trying to generate a heatmap using the "Differential Abundance" tab.

Steps to Reproduce:

1. Navigate to the Differential Abundance tab.
2. After running the DE, Go to Heatmap.
3. Press "Submit" to create a heatmap.

After pressing "Submit", it gave two errors:
a) in the UI:
Error: NA/NaN/Inf in foreign function call (arg 10)

b) in the cmd:
Warning: Error in hclustfun: NA/NaN/Inf in foreign function call (arg 10)
107: %||%
104: modify_list
103: config
101: renderPlotly [\amica\amica/server.R#1571]
100: func
97: shinyRenderWidget
96: func
83: renderFunc
82: output$compareHeatmap
1: runApp

The "Download heatmap data" function appears to work correctly. However, upon inspection of the downloaded data, there are several NA values present in the table. This might be related to the error encountered.

Regards,
Bola

Hello,

I've encountered an issue where an "X" prefix gets added to sample names when I upload the experimental design file.

Below is a screenshot from the original .txt file, where the sample names don't have the "X" prefix:

However, when uploaded to the amica server, the "X" prefix appears:

Is there any workaround for this issue? The prefix also gets carried over to the graphs, which is not ideal.

Thank you for your assistance!

Dear amica developer team,
Thank you for developing this really useful tool. The design and implementation of the shiny app is nicely done.
Have you tested amica for DIA data? In particular, I am interested in analyzing DIA output from Spectronaut.
Thanks

Implement Dot plots, from https://prohits-viz.org/help/analysis/dotplot:

Dot plots have the advantage over heat maps in that they use the same amount of space but visualize more information. In addition to raw quantitative values being displayed via coloured circles, dot plots display the relative readout measurement between conditions via circle size and confidence in the measurement via coloured edge. Heat maps, however, are better for presenting very large data sets as the detailed information of a dot plot gets lost in these instances.

Things to consider

• User defined significance thresholds (p-value vs adj.p-value)
• Pilots without p-values
• Adjustable color gradients (log2FCs)
• User selection: group comparisons
• Hier. clustering (user def. row and column order as input?)
• Relative abundance: intensities and/or avg. spectral counting (e.g select option?)

Hello and great work on this tool! Hope that you are able to get this published very soon :)

I would like to request a new feature for the enrichment analysis. Could you please have the genes from the input that are associated with each enrichment term be output in a column in the output table? This would be great to know which genes are the reason for a certain enrichment.

Thanks!

This issue was already resolved, see (#15).

But somehow the functionality on the server is completely broken when this fix was applied, hence the version on the server does curr. not support FragPipe v18 output yet.
This does not effect the code on github, running locally should work without issues!
Hopefully, this will be soon resolved. Something must have gone wrong with docker build, the code seems fine.

The full functionality is back again on the public server. Very sorry!

Best,
Sebastian

I just wanted to quickly express my gratitude for your great tool. I really enjoy using is.
I would only like to suggest to enable different types of depicting protein profile plots across several samples. It would be great if you could enable to depcit all individaul data points in each sample. Another great way to depcit the profile plots, would be via violin plots.

For getting a large user base, I think it would be good for this tool to function indepentently on Rstudio etc. I am a little familiar with non R coding and was suffering/troubleshooting a lot to get it running and feel this may be a high entry barrier for people.
Howver, I think it was worth it ;)
Cheers

Hello again,
I just wanted to report a minor bug, which I've encountered: It's not possible for me to label individual proteins in the QC correlation dot plots. I can use the selection tools, however no labels appear.

Suggestion (not demand :D):
In regards to the volcano plots, it would be really nice if it was possible to fix labeled protiens in the volcano, so that it's possible to fine tune the labeling.
Best
Andree

Hi,

I managed to upload correctly data from DIA-NN but when I click on analyze the app crashes and the console prints the following error

Warning: Error in :: argument of length 0

Is there anything I'm missing?

Thanks
Lucio

Hello,

During a recent data analysis, I observed that the RawIntensity values in the exported amica file are identical to the ImputedIntensity values. This occurred after a run with vsn normalization and no imputation.

Steps to Reproduce:

1. Conduct a run with vsn normalization.
2. Ensure no imputation is selected.
3. Export the amica file.
4. Inspect the values of RawIntensity and ImputedIntensity.

I suspect this behavior might be a bug. Would you be able to provide clarification or confirm the issue?

Kind Regards, Bola

Add option to choose only quantified proteins as background gene list in over-representation analysis.
By default, all protein-coding genes are considered as background.

Hi I am trying to analyse my data from MQ and getting the following error "error in limma Error in names(x) <- value: 'names' attribute [2] must be the same length as the vector [0]" could you please tell me what the problem could be?

Also, the example files are in .csv format and Amica asks for tsv files. Is it possible to change that?

Hi, when running the app on RStudio I get the following warning "Warning in is.call(funBody[[idx]]) && as.character(funBody[[idx]][[1]]) == :
'length(x) = 3 > 1' in coercion to 'logical(1)'" repeatedly in the console and I can't visualize the table with the differentially expressed proteins, but all the figures are produced normally. Could you help solving this issue?
Thanks

Feature request:
Add the option to download the underlying heatmap data.

Hi Sebastian,

I have a custom output file from DIA-NN. It seems to be getting uploaded successfully but when I press analyze it says no data uploaded. I have attached the files here. Could you please tell me what could be the problem?

Thanks
Maithy

amica_groups.txt
amica_specification.txt
Pel_Amica_Example.txt
amica_expt.txt

Hello,

when trying to upload DIA-NN output, this error pops up:
"simpleWarning in readLines(inFile$datapath, n = 1): line 1 appears to contain an embedded nul"

How to fix it?

Thanks

Is this software compatible with Fragpipe TMT experiments?

Hi,
Firstly let me say i think this tool looks amazing. I am struggling a bit with the input formats however. I have an output from DIA-NN (report.pg-matrix.tsv), which contains proteinID, gene name and LFQ intensity for my runs. I have formatted this into the format required for custom file upload, including a specifications file to let amica know my headers. When i click analyze, i get a small popup in the right corner saying "no data uploaded". I am not sure what to make of this (amica reports upload complete when i add the proteingroups.txt and other files).
I would process with fragpipe or something else if that was easier, but to my knowledge fragpipe does not yet support DIApasef data.
Thanks in advance
Silas

Hi Sebastian,

I was asked by a user of Amica if it would be possible to add an additional protein selection option to the Volcano plot in the "Differential abundance" tab? Specifically, it would be useful to have the option to manually submit a list of protein identifiers (Uniprot IDs, Gene names, ...), which are then highlighted and labeled in the volcano plot, similar to what is happening if you use the selection tool. Optimally, the highlighted dots would be plotted above the other points and highlighted with a different color.

Please let me know if it is possible to add this feature.

Best,
David

Hi Sebastian,

Is it possible to implement another significant cutoff other than the ones available? It is called Xiao correction. Here is the link to the paper.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957066/

Thanks
Maithy

Hello,

I encountered an error when trying to generate a dotplot in the "Differential Abundance" tab.
In the UI: it shows in red: Error: 'list' object cannot be coerced to type 'double'
In the cmd:
Warning: Error in dist: 'list' object cannot be coerced to type 'double'
171:
170: stop
169: dotplot
168: renderPlot [\amica\amica/server.R#1174]
166: func
126: drawPlot
112: reactive:plotObj
96: drawReactive
83: renderFunc
82: output$dotplot
1: runApp

Thanks for your help.

Regards,
Bola

Hello,

I am using Amica for the first time. I've uploaded my data (QC'ed MetaMorpheus output) using the custom format option as well as the experimental design, contrast matrix, and specification file. However, after hitting upload I do not get an error and the application appears to be frozen. It is unclear if it is running and even after several hours looks the same. Can you please advise?

Thank you.

Hello,

I tried to adjust the order of samples on the x-axis for the QC & intensity plots from here

but unfortunately this is not reflected in the graph as shown here:

am I missing something here?

Thank you so much for your appreciated help.

Best Regards,
Bola

HI,
I have t output from DIA-NN, would you able to help for correct formatting.

Protein.Group | Protein.Ids | Protein.Names | Genes | First.Protein.Description | 388 | 399 | 404 | 405 | 407 | 408
388 _Control
399_Control
404_Control
405_KO
407_KO
408_KO

Best,