[BioC] SAM analysis of two color microarray data

[James W. MacDonald]

On Thu, Sep 4, 2014 at 12:29 PM, Shan-e-Ahmed Raza [guest] <
guest at bioconductor.org> wrote:

> Dear Biconductor,
>
> I am new to analysis of micro array data and I am trying to analyse a two
> colour micro array data.
> I was trying to  reproduce the results in the paper (
> http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-120/ ). In this
> paper, the authors say that they have normalized the data using 1.  print
> tip loess method and 2.  performed analysis using SAM.
>
> 1.      From limma package userguide, I understand that we cannot perform
> print tip loess normalization on Agilent arrays, therefore, I have
> performed loess normalization.
>
> Currently, I have run following code in R
>
> targets <- readTargets("Psamples.txt")  # Psamples contains the file list
> from raw data.
> RG <- read.maimages(targets, source="agilent")
> RGb0 <- backgroundCorrect(RG, method="none")
> MA0 <- normalizeWithinArrays(RGb0, method="loess") #Normalization using
> loess method
>
> 2.      I have found that the siggenes can be used to perform SAM analysis
> on array express data. The sam function requires data in the form of
> matrix/data frame or expressionset object. The second input required by sam
> is cl which is class labels.
>
> I have used following command to perform SAM analysis
>
> sam.analyse = sam(MA0$M,MA0$genes$ControlType)
>
> as according to my understanding MA0$M contains the normalized data and
> MA0$genes$ControlType contains the class labels.
> But I am getting the error: The length of cl must be equal to the number
> of columns of data. I am not sure how to correct it.
>

The first step is to make sure that your understanding is actually correct.

What do you get from

MA0$genes$ControlType

and

ncol(MA0$M)

Best,

Jim



>
> Please can you confirm how can I use data to perform the analyses. Is
> there anything I am doing wrong?
>
> Regards,
>
>
>  -- output of sessionInfo():
>
> targets <- readTargets("Psamples.txt") # Psamples contains the file list
> from raw data.
> > RG <- read.maimages(targets, source="agilent")
> Read 251486817346_1.txt
> Read 251486817346_2.txt
> Read 251486817346_3.txt
> Read 251486817346_4.txt
> > RGb0 <- backgroundCorrect(RG, method="none")
> > MA0 <- normalizeWithinArrays(RGb0, method="loess")
> > sam.analyse = sam(MA0$M,MA0$genes$ControlType)
> Error in adjust.for.mt(data, cl, var.equal = var.equal) :
>   The length of cl must be equal to the number of columns of data.
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]