Question: lmFit only deals with numerical values (data matrix object)?
0
8.2 years ago by
Peter Davidsen210 wrote:

Hi List

Does "lmFit" in limma only deals with numeric values (positive numbers)? I have created a data matrix object with log2 ratio data (some data assume negative values). Can I use my data matrix as object in the lmFit function?

Kind regards
Peter

limma lmfit • 1.1k views
modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Peter Davidsen210

Hi List

Does "lmFit" in limma only deals with numeric values (positive numbers)? I have created a data matrix object with log2 ratio data (some data assume negative values). Can I use my data matrix as object in the lmFit function?

Kind regards
Peter

ADD REPLYlink modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Peter Davidsen210
Answer: C: lmFit only deals with numerical values (data matrix object)?
1
8.2 years ago by
Holger Schwender900 wrote:

Numeric values do not necessarily need to be positive. They can also be negative. So you can use your log2 ratios as they are (no matter whether they are positive or negative).

Holger

Answer: C: lmFit only deals with numerical values (data matrix object)?
0
8.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Hi, Peter.

You should read the help for lmFit, but to answer your question, yes a numeric matrix can be used for lmFit.

Sean

Answer: C: lmFit only deals with numerical values (data matrix object)?
0
8.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Hi, Peter.

You should read the help for lmFit, but to answer your question, yes a numeric matrix can be used for lmFit.

Sean

Hi Sean,

I read it, but wasn't 100% sure!

Okay, as microarray data need to be log-transformed in order to compare gene activities -
Could I then, if I want to use the lmFit function in limma:
1) transform all my log2 ratio data in my data matrix into fold change - 2^(log2 ratio)
2 divide fold change by 100 => decimal numbers
3) add the value +1 to all decimal numbers
4) log2 transform all decimal numbers (=> all expression values now numerical)

Sorry for the obvious questions, but I'm new to chip analysis, and thus quite unsure

Kind regard

ADD REPLYlink modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Peter Davidsen210

Hi Sean,

I read it, but wasn't 100% sure!

Okay, as microarray data need to be log-transformed in order to compare gene activities -
Could I then, if I want to use the lmFit function in limma:
1) transform all my log2 ratio data in my data matrix into fold change - 2^(log2 ratio)
2 divide fold change by 100 => decimal numbers
3) add the value +1 to all decimal numbers
4) log2 transform all decimal numbers (=> all expression values now numerical)

Sorry for the obvious questions, but I'm new to chip analysis, and thus quite unsure

Kind regard

ADD REPLYlink modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Peter Davidsen210
1

Hi, Peter.

You simply need log ratio data as the input to limma. There is no need to perform the steps above if you are starting with log ratios.

I would suggest working through the excellent Limma User Guide very carefully and be sure to read a little about R along the way.

Sean

ADD REPLYlink modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Sean Davis21k

Hi, Peter.

You simply need log ratio data as the input to limma. There is no need to perform the steps above if you are starting with log ratios.

I would suggest working through the excellent Limma User Guide very carefully and be sure to read a little about R along the way.

Sean

ADD REPLYlink modified 4.5 years ago by Gordon Smyth37k • written 8.2 years ago by Sean Davis21k