Question

LIMMA - for Microarrays?

0

Entering edit mode

jonathan_paul • 0

@7db9f089

Last seen 2.7 years ago

Can I ask - I understand that Limma - Voom has been created for RNA -seq --> do you know if it is suitable to be used for micro arrays as well, since LIMMA was created for microarrays anyway?

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

limma • 1.2k views

ADD COMMENT • link written 2.7 years ago by jonathan_paul • 0

1

Entering edit mode

It is (limma, not the voom transformation), just read the manual.

ADD REPLY • link 2.7 years ago ATpoint ★ 4.0k

0

Entering edit mode

I have, but I am trying to use limma.eu on galaxy to work on microarray data and the main method is voom so I am wondering if this is fine too.

ADD REPLY • link 2.7 years ago jonathan_paul • 0

0

Entering edit mode

what do you think?

ADD REPLY • link 2.7 years ago jonathan_paul • 0

0

Entering edit mode

Cross-posted: https://www.biostars.org/p/9487006/

ADD REPLY • link 2.7 years ago Kevin Blighe ★ 3.9k

0

Entering edit mode

Kevin do you have a suggestion?

ADD REPLY • link 2.7 years ago jonathan_paul • 0

score 1 · Answer 1 · 2021-08-29

1

Entering edit mode

Gordon Smyth 50k

@gordon-smyth

Last seen 59 minutes ago

WEHI, Melbourne, Australia

You absolutely cannot use voom on microarray data, it is only for sequencing data, not for microarrays.

If galaxy has poor support for microarrays, what about trying limma directly in R? Then you can use the full range of capabilities.

ADD COMMENT • link 2.7 years ago Gordon Smyth 50k