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” [image]

How to implement Limma package in R snippet on Knime

mlauber71 February 4, 2024, 11:29am 2

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

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