Hi all, I recently joined a lab and I am currently learning how to perform quality control on microarray gene expression data. I am very new at this and I have been following the methodology used by a previous project at the lab (according to Item 3.2 here).
I am currently trying to perform MDS clustering on my microarray gene expression data in order to separate samples based on their gender. Based on the methods, I am supposed to be able to see two distinct clusters. However, when trying it out on my own in R using limma, I can only acquire a single cluster. How exactly should I go about doing this?
Here is my R code:
library(limma)
expression_data <- t(rma_transposed) # my gene expression data after RMA, with samples in columns and probesets in rows
mds <- plotMDS(expression_data, gene.selection = "common")
plot(mds)
The resulting plot has only a big cluster in the middle, whereas the 'correct' plot has two distinct clusters. Does anyone have any suggestions on what I'm doing wrong? Thank you!
