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
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
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, 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
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
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
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
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version 2.3.6
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