[BioC] [maSigPro] two color array analysis of time series in different cell lines.???
James W. MacDonald
jmacdon at uw.edu
Wed Oct 9 15:10:51 CEST 2013
Hi Neeraj,
On Wednesday, October 09, 2013 8:09:45 AM, Neeraj Rana wrote:
> I want to use maSigPro package for cell line data treated at different time
> points.
> i have three cell lines(HF,HT,NLT),treated on 3 time points
> separately(1,4,12hrs).
> I want to make comparison (HF vs HT),(HF vs NLT),(HT vs NLT).
> I am using M value for comparison produced by limma after normalization.
> I followed the given commands and i am stucked at this error given below.
>
> library(limma)
> library(maSigPro)
> data <- read.maimages(targets,source="agilent")
>> MAW <- normalizeWithinArrays(data,method="loess",bc.method="subtract")
>> edesign.abiotic <-read.table ("edesignabiotic.txt",header=TRUE)
>> names(MAW)
> [1] "targets" "genes" "source" "M" "A"
>> data.abiotic<- MAW$M
>> mat
> FileName Time Replicate HF HT NLT
> 1 1hr_HF_1_7411_1_1 1 1 1 0 0
> 2 1hr_HF_2_7411_1_3 1 1 1 0 0
> 3 4hr_HF1_7411_1_2 4 2 1 0 0
> 4 4hr_HF_2_7411_1_4 4 2 1 0 0
> 5 12hr_HF_1_7357_1_1 12 3 1 0 0
> 6 12hr_HF_2_7357_1_2 12 3 1 0 0
> 7 1Hr-HT-2_7356_1_3 1 4 0 1 0
> 8 1Hr-HT_1_7356_1_1 1 4 0 1 0
> 9 4Hr-HT-1_7356_1_2 4 5 0 1 0
> 10 4Hr-HT-2_7356_1_4 4 5 0 1 0
> 11 12hr_HT_1_7357_1_3 12 6 0 1 0
> 12 12hr_HT_2_7357_1_4 12 6 0 1 0
> 13 N_LT_207_1_3_1HR 1 7 0 0 1
> 14 N_LT_207_1_4_1HR 1 7 0 0 1
> 15 N_LT_207_1_1_4HR 4 8 0 0 1
> 16 N_LT_207_1_2_4HR 4 8 0 0 1
> 17 N_LT_8052_1_3_12HR 12 9 0 0 1
> 18 N_LT_8052_1_4_12HR 12 9 0 0 1
>> design <- make.design.matrix(mat, degree = 2, time.col = 2,repl.col = 3,
> group.cols = c(4:ncol(mat)))
>
>> names(design)
> [1] "dis" "groups.vector" "edesign"
>
>> design$groups.vector
> [1] "HTvsHF" "NLTvsHF" "HF" "HTvsHF" "NLTvsHF" "HF" "HTvsHF"
> "NLTvsHF"
>
>> dim(design$dis)
> [1] 18 8
>> names(design$dis)
> [1] "HTvsHF" "NLTvsHF" "Time" "TimexHT" "TimexNLT" "Time2"
> "Time2xHT" "Time2xNLT"
>> names(design$edesign)
> [1] "FileName" "Time" "Replicate" "HF" "HT" "NLT"
>
>> fit <- p.vector(data.abiotic, design, Q = 0.05, MT.adjust = "BH", min.obs
> = -14)
I would imagine the problem is the argument you are passing for
min.obs. Did you intend to pass in a negative number? If so, why?
Best,
Jim
> Error in dat[, as.character(rownames(dis))] : subscript out of bounds
>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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