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joannawolthuis / MetaboShiny

Repository for MetaboShiny, a novel R and RShiny based metabolomics data analysis package.
https://www.biorxiv.org/content/10.1101/734236v1
Apache License 2.0
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Normalization Failed Error #51

Closed xjallen closed 3 years ago

xjallen commented 3 years ago

I'm bringing my own data into MetaboShiny and can't seem to normalize it. I receive the error "Error in [.data.table(metshiCSV, , ..condition) :column(s) not found: NA"

Do you know what is causing this error to be thrown up?

joannawolthuis commented 3 years ago

Hi! It seems like a metadata problem, can you give an idea of what your metadata looks like?

xjallen commented 3 years ago

My metadata contains presence/absence data for microbial treatments as well as plant physiological responses, so a mix of both numerical and non-numerical data. These are in addition to the sample and individual columns that are required.

joannawolthuis commented 3 years ago

Hi there! I kind of need a dummy (maybe a scrambled?) version of your metadata to estimate what the problem is - the error is at a point where it looks for a 'default' experimental variable to use (at least 2 groups, but as few as possible) so i expect the problem is in that possibly the metadata is in a (slightly) wrong format.

xjallen commented 3 years ago

I've emailed you a dummy matrix. Apologies if that's inconvenient, but I couldn't think of a better way to get it to you. Thanks!

joannawolthuis commented 3 years ago

That's perfect, thank you! To test the fix, are you working on the Docker ver. or on your own R version?

Op di 29 dec. 2020 om 19:08 schreef xjallen notifications@github.com:

I've emailed you a dummy matrix. Apologies if that's inconvenient, but I couldn't think of a better way to get it to you. Thanks!

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xjallen commented 3 years ago

I am working on the R version.

joannawolthuis commented 3 years ago

Alright, great. Would you mind trying out the dev branch to see if it fixes your problem? I do ask for your patience, I was working on rolling it out to master branch soon so there might be some bugs (but hopefully not the one you mention here :) )

xjallen commented 3 years ago

I'm trying to install the dev branch, but hit an error stating "Error : (converted from warning) unable to re-encode 'oxy-wrapper_functions.R' line 1568"

joannawolthuis commented 3 years ago

Hmm, I tried a fix, would you mind trying again? Thanks :)

Op wo 30 dec. 2020 om 00:53 schreef xjallen notifications@github.com:

I'm trying to install the dev branch, but hit an error stating "Error : (converted from warning) unable to re-encode 'oxy-wrapper_functions.R' line 1568"

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joannawolthuis/MetaboShiny/issues/51#issuecomment-752279485, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAG4ZKEJTK5AIEFASMRARLSXJTXFANCNFSM4VEOV3LQ .

xjallen commented 3 years ago

I've got the dev branch installed, however it fails on startup. The error reads: Warning: Error in list.files: invalid 'path' argument 46: list.files 45: [reactive/patientdbs.R#8] 2: shiny::runApp 1: MetaboShiny::start_metshi

joannawolthuis commented 3 years ago

Cannot reproduce this one, but I tried a fix, please give it a try! Are you working on Windows? Might continue debugging on my Windows PC if so.

Op do 31 dec. 2020 om 00:13 schreef xjallen notifications@github.com:

I've got the dev branch installed, however it fails on startup. The error reads: Warning: Error in list.files: invalid 'path' argument 46: list.files 45: [reactive/patientdbs.R#8] 2: shiny::runApp 1: MetaboShiny::start_metshi

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xjallen commented 3 years ago

I am working on Windows. I'm getting a combination of errors now: Warning: Error in [[: subscript out of bounds 45: [D:\xvsal\R\win-library\4.0\MetaboShiny/server.R#296] 2: shiny::runApp 1: MetaboShiny::start_metshi Warning: Error in dir.exists: invalid filename argument 46: dir.exists 45: [reactive/patientdbs.R#8] 2: shiny::runApp 1: MetaboShiny::start_metshi

joannawolthuis commented 3 years ago

Alright, thank you again! I switched to Windows and got it running properly on that PC. Please try the dev branch again once you have time!

Op do 31 dec. 2020 om 19:35 schreef xjallen notifications@github.com:

I am working on Windows. I'm getting a combination of errors now: Warning: Error in [[: subscript out of bounds 45: [D:\xvsal\R\win-library\4.0\MetaboShiny/server.R#296] 2: shiny::runApp 1: MetaboShiny::start_metshi Warning: Error in dir.exists: invalid filename argument 46: dir.exists 45: [reactive/patientdbs.R#8] 2: shiny::runApp 1: MetaboShiny::start_metshi

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xjallen commented 3 years ago

Ok! I've got the dev branch installed and working. Unfortunately I'm hitting errors when ingesting the data. The error reads: [1] "Importing neg mode peaks!" Error in peaklists[[which(isNonEmpty)]] : attempt to select less than one element in get1index.

The example data included with MetaboShiny doesn't cause this error, so I'm guessing that something is wrong with my peak data...

joannawolthuis commented 3 years ago

I fear so yes :( in which ways does your format differ from the example? Again dummy input data would be great for me to help, if you have it :)

On Fri, Jan 1, 2021, 8:15 PM xjallen notifications@github.com wrote:

Ok! I've got the dev branch installed and working. Unfortunately I'm hitting errors when ingesting the data. The error reads: [1] "Importing neg mode peaks!" Error in peaklists[[which(isNonEmpty)]] : attempt to select less than one element in get1index.

The example data included with MetaboShiny doesn't cause this error, so I'm guessing that something is wrong with my peak data...

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joannawolthuis/MetaboShiny/issues/51#issuecomment-753370097, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAG4ZPQYF7Z37NT6MNFMODSXYNNPANCNFSM4VEOV3LQ .

xjallen commented 3 years ago

I don't notice any obvious differences in the format, but I could easily be wrong. I've emailed you a dummy datasheet. Thanks for all the help!

joannawolthuis commented 3 years ago

Thanks! I imported your data OK now. Can you try dev again? :)

Op za 2 jan. 2021 om 18:53 schreef xjallen notifications@github.com:

I don't notice any obvious differences in the format, but I could easily be wrong. I've emailed you a dummy datasheet. Thanks for all the help!

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xjallen commented 3 years ago

I've finally gotten around to trying it out and the data are imported without errors! Normalization however does not work with my data nor the example data the error reads:

Error in colSums(mSet$dataSet$missing) : 'x' must be an array of at least two dimensions

joannawolthuis commented 3 years ago

Found the cause - my MetaboanalystR version was one behind the newest. Will start forcing specific version soon, haha! Please take a look and let me know.

Op do 7 jan. 2021 om 06:19 schreef xjallen notifications@github.com:

I've finally gotten around to trying it out and the data are imported without errors! Normalization however does not work with my data nor the example data the error reads:

Error in colSums(mSet$dataSet$missing) : 'x' must be an array of at least two dimensions

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joannawolthuis/MetaboShiny/issues/51#issuecomment-755890658, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAG4ZKP2SUYGIK75PNTTCDSYU76TANCNFSM4VEOV3LQ .

xjallen commented 3 years ago

I believe you've addressed all of my issues! All of my data are being imported properly, normalized, and analyzed! Thanks a lot!