Entering edit mode
Dear Priyanka,
On the quick read through, I don't see any problems with your code.
It
should work perfectly as far as I can see. Can you please give us the
output of
dimMA.Aq)
and
dim(design)
at the time of the error.
Best wishes
Gordon
> Date: Sun, 2 Jan 2011 22:00:06 -0600 (CST)
> From: "Kachroo, Priyanka" <priya_coll at="" neo.tamu.edu="">
> To: bioconductor at r-project.org
> Subject: [BioC] two color time course analysis
> Message-ID: <200725487.382131294027206350.JavaMail.root at neo-
mail-3>
> Content-Type: text/plain; charset=utf-8
>
> Hi All,
>
> I would like to ask the forum the best statistical analysis approach
for
> my experimental design in which i have three time points T0, T6 and
T12
> for a treatment group. I need to evaluate the DE genes between T6&T0
and
> also T12&T0. Since the same set of animals were involved at all
three
> time points, will a paired t-test for T6-T0 and T12-T0 be a better
> strategy or a time course analysis.
>
> I have dual color arrays hybridized in the following format. I tried
to
> do a time series analysis by first separating the channels and then
> setting the contrasts as depicted in limma manual for single color
> arrays (section 8.8 in limma manual). However i get following error:
> "Error in intraspotCorrelationMA.Aq, design) : The number of rows
of
> the design matrix should match the number of channel intensities,
i.e.,
> twice the number of arrays".
>
> Target file:
> SlideNumber FileName Cy3 Cy5 Identity
> 14117071 14117071.gpr T6 T0 61
> 14117070 14117070.gpr T6 T0 123
> 14116987 14116987.gpr T6 T0 308
> 14117067 14117067.gpr T0 T6 315
> 14117099 14117099.gpr T0 T6 319
> 14116988 14116988.gpr T0 T12 61
> 14116990 14116990.gpr T0 T12 123
> 14116964 14116964.gpr T0 T12 308
> 14116989 14116989.gpr T12 T0 315
> 14116948 14116948.gpr T12 T0 319
>
> Here is code used so far:
>> targets<-readTargets("targets.txt")
>> RG<-read.maimages(targets,source="genepix",columns=list(R="F635
Median",G="F532 Median",Rb="B635",Gb="B532"))
> Read 14117071.gpr
> Read 14117070.gpr
> Read 14116987.gpr
> Read 14117067.gpr
> Read 14117099.gpr
> Read 14116988.gpr
> Read 14116990.gpr
> Read 14116964.gpr
> Read 14116989.gpr
> Read 14116948.gpr
>> RG$genes<-readGAL()
>> spottypes<-readSpotTypes("Spottypes.txt")
>> RG <- backgroundCorrect(RG, method="normexp", offset=50)
> Green channel
> Corrected array 1
> Corrected array 2
> Corrected array 3
> Corrected array 4
> Corrected array 5
> Corrected array 6
> Corrected array 7
> Corrected array 8
> Corrected array 9
> Corrected array 10
> Red channel
> Corrected array 1
> Corrected array 2
> Corrected array 3
> Corrected array 4
> Corrected array 5
> Corrected array 6
> Corrected array 7
> Corrected array 8
> Corrected array 9
> Corrected array 10
>> MA.p <- normalizeWithinArrays(RG)
>> MA.Aq<-normalizeBetweenArrays(MA.p,method="Aquantile")
>> targets2<-targetsA2C(targets)
>> targets2
> channel.col SlideNumber FileName Identity Target
> 1.1 1 14117071 14117071.gpr 61 T6
> 1.2 2 14117071 14117071.gpr 61 T0
> 2.1 1 14117070 14117070.gpr 123 T6
> 2.2 2 14117070 14117070.gpr 123 T0
> 3.1 1 14116987 14116987.gpr 308 T6
> 3.2 2 14116987 14116987.gpr 308 T0
> 4.1 1 14117067 14117067.gpr 315 T0
> 4.2 2 14117067 14117067.gpr 315 T6
> 5.1 1 14117099 14117099.gpr 319 T0
> 5.2 2 14117099 14117099.gpr 319 T6
> 6.1 1 14116988 14116988.gpr 61 T0
> 6.2 2 14116988 14116988.gpr 61 T12
> 7.1 1 14116990 14116990.gpr 123 T0
> 7.2 2 14116990 14116990.gpr 123 T12
> 8.1 1 14116964 14116964.gpr 308 T0
> 8.2 2 14116964 14116964.gpr 308 T12
> 9.1 1 14116989 14116989.gpr 315 T12
> 9.2 2 14116989 14116989.gpr 315 T0
> 10.1 1 14116948 14116948.gpr 319 T12
> 10.2 2 14116948 14116948.gpr 319 T0
>> lev<-c("T0","T6","T12")
>> u<-unique(targets2$Target)
>> f<-factor(targets2$Target,levels=lev)
>> design<-model.matrix(~0+f)
>> colnames(design)<-lev
>> corfit<-intraspotCorrelationMA.Aq,design)
> Error in intraspotCorrelationMA.Aq, design) :
> The number of rows of the design matrix should match the number of
channel intensities, i.e., twice the number of arrays
>>
>
> Can someone please help me with this error and how to obtain
> differentially expressed genes for contrasts "T6-T0" and "T12-T0".
>
>
> Regards
>
> Priyanka Kachroo
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