Dear all,
I have an Affy time course experiment as follows:
0hr - 2hr - 4hr, I have 2 replicates for the 2hr and 4hr and only one
(chip) for 0hr. Would I be able to analyze this experiment using
limma? (I know its not a good idea).
Actually I tried analyzing this in limma, and got the following error
when constructing contrasts:
Error in parse(file, n, text, prompt) : parse error
I am assuming this is due to the design matrix having only one chip
for the 0hr time point. Thanks for your suggestions/advice.
Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076
On 3/14/06 3:19 PM, "Khan, Sohail" <khan at="" cshl.edu=""> wrote:
> Dear all,
>
> I have an Affy time course experiment as follows:
> 0hr - 2hr - 4hr, I have 2 replicates for the 2hr and 4hr and only
one (chip)
> for 0hr. Would I be able to analyze this experiment using limma? (I
know its
> not a good idea).
> Actually I tried analyzing this in limma, and got the following
error when
> constructing contrasts:
> Error in parse(file, n, text, prompt) : parse error
> I am assuming this is due to the design matrix having only one chip
for the
> 0hr time point. Thanks for your suggestions/advice.
Sohail,
You can do this in limma. The parse error is most likely due to the
way you
constructed the call to makeContrasts. Perhaps you would like to post
the
code that you are using to make your design matrix and the contrast
matrix,
along with the output and errors?
As an aside, you probably want to get in the habit of posting
sessionInfo()
when you post to the list. It really does help in many cases.
Sean
