0
$\begingroup$

I am very new to bioinformatics but have some background in coding with R. I have been asked to find a data set and complete differential expression using the Limma package in R. I have tried a few data sets but haven't been able to get any code to work.

What kind of data do I need to have in order for Differential Expression to work with Limma R? I have tried load and read.table, is there a read function that I am missing?

I was advised to look on Gene Expression Omnibus to find published data sets to work on but again I am struggling to find any that will work.

Thank you

Improve this question
$\endgroup$
3
  • $\begingroup$ Thanks Sabrina, there is a recent Limma question which might help. Please could you supply the code you have tried and resulting error? I don't use Limma but it will almost certainly have a test data set. For example "16 Two-Color Case Studies" in the manual bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/… $\endgroup$
    – M__ ♦
    Commented Jul 18, 2023 at 15:19
  • 1
    $\begingroup$ Thank you so much for your help. I am pretty sure its the kind of data I am trying to input, I tried to use exprs() for my data and even that pulls up a data type error $\endgroup$
    – Sabrina
    Commented Jul 18, 2023 at 15:38
  • $\begingroup$ Showing your code will help. There isn't many here who use Limma, but let's see. Also keep in mind not to confuse Limma with Limma-voom. $\endgroup$
    – M__ ♦
    Commented Jul 18, 2023 at 15:55

1 Answer 1

Reset to default
0
$\begingroup$

Limma is relatively generic in what it accepts. Typically it is either data on log2 scale that are either already normalized or need some of the inbuilt normalization methods (such as quantile normalization), or in case of RNA-seq you can provide raw counts which then can run through the limma-voom pipeline.

The format is always a matrix of counts/values, with genes/observations in rows and samples/specimen in columns.

For practice, you could follow the RNA-seq/limma-voom section (chapter 15) of the limma manual which has a RNA-seq case study available at https://subread.sourceforge.net/RNAseqCaseStudy.html with example data and code.

GEO has a lot of published data, often microarray gene expression values or RNA-seq, but lets discuss this in a separate question if you need it to keep this here focused on limma.

Improve this answer
$\endgroup$
1
  • $\begingroup$ Thank you very much for your help, I managed to find some data on GEO that I could practice on and its working with the code that I knew worked already since I had used it in a code along tutorial $\endgroup$
    – Sabrina
    Commented Jul 20, 2023 at 8:40

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.