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

[James W. MacDonald]

Hi Neeraj,

The argument for min.obs is described as:

"genes with less than this number of true numerical values will be 
excluded from
the analysis. Default is 3 (minimun value for a quadratic fit)"

So the argument isn't the minimum expression value, but rather the 
minimum number of observations required for a gene to be used in the 
analysis.

Best,

Jim



On Wednesday, October 09, 2013 9:32:12 AM, Neeraj Rana wrote:
> hi jim,
> thanks for your response to query.
> As i understood from tutorial min.obs is used for gene expression
> value(minimum expression value).But as i am using fold change (M=R\G)
> instead of expression value so  the fold change will be in negative
> also for down regulated genes.So i passed the value in negative for
> min.obs.
>
> thanks.
>
>
>
>
> On Wed, Oct 9, 2013 at 6:40 PM, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>> wrote:
>
>     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
>
>                 [[alternative HTML version deleted]]
>
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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
>
>
>
>
> --
> Neeraj Kumar
> Prof. Kondaiah' Lab
>
>
>       Molecular Reproduction Development and Genetics
>
> Indian Institute of Science
> Bangalore 560012
> Mobile # +91-9986295625

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