idrblab / noreva Goto Github PK

Basic information

My operating system: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz 2.21 GHz, 16.0 GB (15.8 GB usable)
My MZmine version: MZmine3.0.21-beta

What happened

"PrepareInuputFiles" and "normulticlassqcall" functions don't work, despite I successfully install all required package on R R version 4.2.0 and formatted CSV table as described in your tutorial.

sample name label _477.065_4.52 12.986_0.74 133.014_0.71 420.046_2.93 439.085_0.68
Aviso_232_CuCl2_Block2.mzXML Sample 1 3.12E-01 1.77E-01 1.05E-01 1.25E-01 1.11E-02
Aviso_233_CuCl2_Block2.mzXML Sample 1 2.70E-01 1.58E-01 1.10E-01 1.43E-01 1.65E-02
Aviso_280_CuCl2_Block3.mzXML Sample 1 2.59E-01 1.92E-01 1.19E-01 1.67E-01 2.27E-02
Chifu_187_CuCl2_Block1.mzXML Sample 2 4.22E-01 2.66E-01 1.02E-01 1.21E-02 1.49E-02
Chifu_231_CuCl2_Block2.mzXML Sample 2 3.94E-01 1.77E-01 1.38E-01 4.83E-02 2.50E-02

Thank you for your help
Anani

Hi!

Thanks for this cool package but I'm facing issues while testing my own data.

I read my data frame with this command:
multi_qcs_data <- PrepareInuputFiles(dataformat = 1, rawdata = "my_dat.csv")

Then I run this command:

normulticlassqcall(fileName = multi_qcs_data, SAalpha="Y", SAbeta="Y", SAgamma="Y")

I got this output and nothing else:

NOREVA is Running ...

---

Depending on the size of your input dataset
Several mintues or hours may be needed for this assessment

---

STEP 1: Prepare input file in standard formats of NOREVA

STEP 2: The assumption(s) held as indicated by users
Study Assumption alpha: all proteins were equally important (Y/N): Y
Study Assumption beta: the level of protein abundance was constant among all samples (Y/N): Y
Study Assumption gamma: the intensity of the majority of proteins were unchanged (Y/N): Y

STEP 3: The criteira selected by users for this assessment
Criterion Ca: Reduction of Intragroup Variation
Criterion Cb: Differential Metabolic Analysis
Criterion Cc: Consistency in Marker Discovery
Criterion Cd: Classification Accuracy

NOREVA is Running ...

Then I re-run the command with normulticlassqcall function and got nothing, it prints nothing to the screen.

My values were float but I converted them to integers so this could not be an issue. I also tried to read the scripts manually you shared on GitHub, deinstall the package and try to run my command like this but it didn't work either. I was also able to analyze my data with your online tool btw.

I'm attaching toy data (toy_data.csv) so you can test it. I'll appreciate it if you can help me with this issue, thanks in advance!

Best regards,

no results, only Errors, can the authors help the users, please

multi_none_data <- read.csv(file = "Timecourse_without_QCSIS.csv", header = TRUE, stringsAsFactors = FALSE)
class(multi_none_data)
[1] "data.frame"
dim(multi_none_data)
[1] 36 127

allranks_non <- normulticlassnoall(fileName = multi_non_data, assum_a="Y", assum_b="Y", assum_c="Y")
Erreur dans normulticlassnoall(fileName = multi_non_data, assum_a = "Y", :
arguments inutilisés (assum_a = "Y", assum_b = "Y", assum_c = "Y")

nordata <- normulticlassmatrix(datatype = 1, fileName = multi_non_data, impt="1", trsf="1", nmal="1", nmal2="1")
NOREVA is Running ...
Erreur dans if (class(imput_m) == "try-error") { :
la condition est de longueur > 1

normulticlassqcall(fileName = multi_qcs_data, SAalpha="Y", SAbeta="Y", SAgamma="Y")
NOREVA is Running ...

returns the empty file "OUTPUT-NOREVA-Record.txt"

Hi.

I am trying to use NOREVA 2.1.1. on Windows 10 22H2, compilation 19045.2846, and on R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle". Platform: x86_64-w64-mingw32/x64 (64-bit).

I used the example data available in http://idrblab.cn/noreva/#part2.4 Multiclass_with_QCS.csv

The code I used is the following:

`

setwd("C:/Users/HANS/Documents/Norevatest")
library(NOREVA)
Carregando pacotes exigidos: rJava
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Prepared_inputdata <- PrepareInuputFiles(dataformat = 1, rawdata = "Multiclass_with_QCS.csv")
normulticlassqcall(fileName = Prepared_inputdata, SAalpha = "Y", SAbeta = "N", SAgamma = "N")
NOREVA is Running ...

Depending on the size of your input dataset
Several mintues or hours may be needed for this assessment

STEP 1: Prepare input file in standard formats of NOREVA

STEP 2: The assumption(s) held as indicated by users
Study Assumption alpha: all proteins were equally important (Y/N): Y
Study Assumption beta: the level of protein abundance was constant among all samples (Y/N): N
Study Assumption gamma: the intensity of the majority of proteins were unchanged (Y/N): N

STEP 3: The criteira selected by users for this assessment
Criterion Ca: Reduction of Intragroup Variation
Criterion Cb: Differential Metabolic Analysis
Criterion Cc: Consistency in Marker Discovery
Criterion Cd: Classification Accuracy

NOREVA is Running ...

`

The command creates a 0 KB file named: OUTPUT-NOREVA-Record.txt. Also, it does not creat the output file: "OUTPUT-NOREVA-Overall.Ranking.Data.csv"

After hours, it seems that nothing happend. But what is even weirder is that it allows inserting more code (e.g. normvisualization function) as if he had finished the processing of the previous code.

Plese, I would like to know how to solve this issue.

Kind regards,

Bug Description

Please describe the bugs

Runtime Environment

• Operation System: Your OS with version, such as Windows 11
• R version: Your R with version, such as R 4.1.2
• Package version: Your installed noreva and other requirement packages' version

Logs

Please paste full log output here

Hi,

I'm using Mac Catalina but I tried this also on Windows and NOREVA does not work in both cases. I downloaded NOREVA and installed all its dependencies in RStudio, with latest versions of R/RStudio. The installation of all dependencies and NOREVA went well. I can load the library without any errors.

I downloaded the 'Multiclass_without_QCSIS.csv' demo file Multiclass_without_QCSIS.csv
from the website and ran the commands as outlined in this tutorial. The PrepareInuputFiles command runs fine but the others don't produce any outputs even after several minutes of waiting. Specifically, I ran the following commands:

library(NOREVA)

peaks <- PrepareInuputFiles(dataformat=1, 
                            rawdata='Multiclass_without_QCSIS.csv')

normulticlassnoall(fileName=peaks, SAalpha="Y", SAbeta="Y", SAgamma="Y") #I also tried running the next command directly without running this command

outmatrix <- normulticlassmatrix(datatype=1, fileName=peaks, impt=2, trsf=2, nmal=20)

write.csv(outmatrix, file='processed-optimal.csv')

I also tried this with my real MS data, which is several thousand peaks. It does not run with that too. There are no error messages but also no R objects or standard output streams produced.

This issue is the same as a previously closed issue: #2