[BioC] [maSigPro] two color array analysis of time series in different cell lines.???

[James W. MacDonald]

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