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@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

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