How to implement Limma package in R snippet on Knime

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.


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))

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”

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

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

df <-
knime.out <-

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