Error with setup_analysis()

[amechakra]

Hi,

I would like to try the vignette. The first steps go well until this one: adata <- setup_analysis(startdata, config)

I get the following error: "creating sampleName Error in if (!after) c(values, x) else if (after >= lengx) c(x, values) else c(x[1L:after], : missing value where TRUE/FALSE needed"

It seems that my data contains missing values but I don't know how to handle them. I tried : data <- read.table("path_to/proteinGroups.txt", sep="\t",na.strings = c(""), header=T) data <- data %>% drop_na(c("Protein.IDs", "Gene.names", "Intensity")) startdata <- prolfqua::tidyMQ_ProteinGroups(data) ...steps up to: adata <- setup_analysis(startdata, config)

but I still get the same error.

Here is the link to my protein groups file: https://www.swisstransfer.com/d/34536145-ba5e-4994-8364-fa2a5aca223a

[wolski]

Dear amechakra,

The missing values are not the problem. Could you tell me how you specified the configuration (config) variable? Could you also share this code? I want to reproduce the error, which would help me to give you an answer and improve the error message.

Witek

[amechakra]

Dear Witek,

Thanks for your prompt answer.

Sorry, I did not specify that I am applying the vignette : "Comparing Two Groups with prolfqua" https://fgcz.github.io/prolfqua/articles/Comparing2Groups.html

Here is the code that gave the error:

inputMQfile <-  file.path("/path_to/proteinGroups.txt")
inputAnnotation <- file.path("path_to/annotation.xlsx")
startdata <- prolfqua::tidyMQ_ProteinGroups(data)
annotation <- readxl::read_xlsx(inputAnnotation)
head(annotation)
startdata <- dplyr::inner_join(annotation, startdata, by = "raw.file")
startdata <- dplyr::filter(startdata, nr.peptides > 1)
atable <- AnalysisTableAnnotation$new()
atable$fileName = "raw.file"
atable$hierarchy[["protein_Id"]] <- c("proteinID")
atable$set_response("mq.protein.intensity")
config <- AnalysisConfiguration$new(atable)
adata <- setup_analysis(startdata, config) #the error comes here

proteinGroups: https://www.swisstransfer.com/d/34536145-ba5e-4994-8364-fa2a5aca223a annotation: https://www.swisstransfer.com/d/75d16e41-28de-4b37-b943-cc422144cc1b

---

From: Witold Wolski @.***> Sent: 21 March 2023 12:17:44 To: fgcz/prolfqua Cc: Mechakra Asma; Author Subject: Re: [fgcz/prolfqua] Error with setup_analysis() (Issue #54)

Dear amechakra,

The missing values are not the problem. Could you tell me how you specified the configuration (config) variable? Could you also share this code? I want to reproduce the error, which would help me to give you an answer and improve the error message.

Witek

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[wolski]

Hi, Thanks for sharing the code and data.

There are two things you need to fix. First, the raw file names in the annotation do not match those coming from tidyMQ_ProteinGroups.

> annotation$raw.file[1]
[1] "20210920_002_S312150_2021-08-17_HuBiceps_LCM_141_Pat1216_Diseased.raw"
> unique(startdata$raw.file)[1]
[1] "02_s312150_2021.08.17_hubiceps_lcm_141_pat1216_diseased"

Then you can check that the join does not return an empty data frame.

startdata <- dplyr::inner_join(annotation, startdata, by = "raw.file")

The second possible problem is that you did not specify that Condition and sample are the columns containing the explanatory variables:

atable <- prolfqua::AnalysisTableAnnotation$new()
atable$fileName = "raw.file"
atable$hierarchy[["protein_Id"]] <- c("proteinID")
atable$factors[["Condition"]] <- "Condition"
atable$factors[["PatientID"]] <- "sample"

Afterward, using prolfqua should become much more straightforward.

I hope this helps.

[amechakra]

Thank you. It perfectly works now.

---

From: Witold Wolski @.***> Sent: 22 March 2023 10:42:53 To: fgcz/prolfqua Cc: Mechakra Asma; Author Subject: Re: [fgcz/prolfqua] Error with setup_analysis() (Issue #54)

Hi, Thanks for sharing the code and data.

There are two things you need to fix. First, the raw file names in the annotation do not match those coming from tidyMQ_ProteinGroups.

annotation$raw.file[1] [1] "20210920_002_S312150_2021-08-17_HuBiceps_LCM_141_Pat1216_Diseased.raw" unique(startdata$raw.file)[1] [1] "02_s312150_2021.08.17_hubiceps_lcm_141_pat1216_diseased"

Then you can check that the join does not return an empty data frame.

startdata <- dplyr::inner_join(annotation, startdata, by = "raw.file")

The second possible problem is that you did not specify that Condition and sample are the columns containing the explanatory variables:

atable <- prolfqua::AnalysisTableAnnotation$new() atable$fileName = "raw.file" atable$hierarchy[["protein_Id"]] <- c("proteinID") atable$factors[["Condition"]] <- "Condition" atable$factors[["PatientID"]] <- "sample"

Afterward, using prolfqua should become much more straightforward.

I hope this helps.

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