How to implement Limma package in R snippet on Knime

[Erzascarlet]

Hello, I am working with a gene expression dataset. In the image below, you can see the structure of my dataset. I am attempting to straightforwardly use the Limma package on my dataset. I am using a CSV reader to read my file, and then I am using an R snippet with the following code to run the Limma package. However, I am encountering different errors, with the error below being the most persistent. Should I be performing more data transformation steps before feeding my data into the R snippet with the limma package? If someone could tell me where I am making a mistake and how I can fix it, it would be great. Or if someone already has an existing limma node for knime for Windows that would be great as well.

code
"

Convert the ‘class’ column to a factor

kIn$class ← factor(kIn$class)

Create a design matrix

design ← model.matrix(~0 + kIn$class)

Extract the expression data

exprs_data ← as.matrix(kIn[, -1]) # Convert to a matrix

Load the limma package

if (!requireNamespace(“BiocManager”, quietly = TRUE))
install.packages(“BiocManager”)
BiocManager::install(“limma”)
library(limma)

Fit the linear model

fit ← lmFit(exprs_data, design)

Apply empirical Bayes moderation

fit ← eBayes(fit)

Extract the results

results ← topTable(fit, coef=“kIn$classpos”, number=nrow(exprs_data))"

This is the error

“ERROR R Snippet 5:489 Execute failed: Failed to evaluate the script:
Error : Error in lmFit(exprs_data, design) :
row dimension of design doesn’t match column dimension of data object”

[mlauber71]

@Erzascarlet welcome to the KNIME forum. Maybe you could provide us with a complete readable code and example:

Dynamic Filter connected to several Python Views of a dashboard

@DanGenEire what would be good is a complete workflow example and a code that is formatted in a readable way or add it as a file. [image] import pandas as pd import numpy as np I will see if I can come up with an example later.

First you might want to check how to bring data to and from an R node.

https://docs.knime.com/latest/r_installation_guide/index.html#_introduction

df <- knime.in
knime.out <- as.data.table(df)

splitting strings into letters using R snippet node

@0nly4phil for the second example as.data.table() as well as a conversion to character seems to do the trick. [image] The transfer is done with “data.table”: [image] df1 <- knime.in df1 <- as.data.frame(df1) a <- as.character(df1$'Column Header') a <- strsplit(a,split="") b <-matrix(unlist(a),ncol=10,byrow=T) df1$'splt'<-b knime.out <- as.data.table(df1) Convert data from KNIME to R and back with split of text column - KNIME Forum (76340).knwf (88.8 KB)