Hi Stanley,
you'll probably want to do something along these lines:
>spotTypes <- readSpotTypes()
which requires that a SpotType.txt file in the current directory.
Contents of the file look like this:
SpotType ID Color
Gene * black
Spikein alien* red
Blank EMPTY yellow
Then before fitting, you can do something like this:
>isGene = MA.p$genes$Status=="Gene"
>fit = lmFit(MA.p[isGene,], design)
Kind regards,
yannick
--------------------------------------------
yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
http://www.unil.ch/dee/page28685_fr.html
On Mar 11, 2008, at 8:43 , Ng Stanley wrote:
> Hi,
>
> I am using limma package to process some gpr files, which contained
> EMPTY
> gene id for specific blocks of rows. Couple of questions
> A) Before what stage should these "EMPTY" rows be deleted. I used
> functions:
> backgroundCorrect, normalizeWithinArrays, lmFit, contrasts.fit,
> eBayes ?
> B) In relation to A), are there any functions in limma that I can
> invoke to
> delete those "EMPTY" rows ?
> C) What are those "EMPTY" rows ?
>
> Thanks
>
> [[alternative HTML version deleted]]
>
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Hi, all,
I have question about the within-array replicates analysis with limma.
The replicates for each spot in my cDNA microarray are irregular-
spaced.
There are 3 replicates for each spot, which are randomly distributed
in
the array. When I entitled "irregular=True, ndup=3, spacing=1", I
thought the space will be counted automatically based on gene IDs.
However, in the output table, I can still find some genes listed twice
with different values (i.e. B values, p-values, etc). Did I do
anything
wrong with that? I went through lots of examples online, and most
samples with replicated spots are regulated spaced. Could you please
tell me what I am supposed to do with this kind of problem? I really
appreciate it. Thanks.
Wei
