[BioC] SAM analysis of two color microarray data

Shan-e-Ahmed Raza [guest] guest at bioconductor.org
Thu Sep 4 18:29:25 CEST 2014


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. 

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.

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