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Question: [maSigPro] two color array analysis of time series in different cell lines.???
0
gravatar for neeraj rana
5.2 years ago by
neeraj rana60
neeraj rana60 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$edesign) [1] "FileName" "Time" "Replicate" "HF" "HT" "NLT" > fit <- p.vector(data.abiotic, design, Q = 0.05, MT.adjust = "BH", min.obs = -14) Error in dat[, as.character(rownames(dis))] : subscript out of bounds [[alternative HTML version deleted]]
ADD COMMENTlink modified 3 months ago by sbbinfo900 • written 5.2 years ago by neeraj rana60
0
gravatar for James W. MacDonald
5.2 years ago by
United States
James W. MacDonald48k wrote:
Hi Neeraj, On Wednesday, October 09, 2013 8:09:45 AM, Neeraj Rana wrote: > I want to use maSigPro package for cell line data treated at different time > points. > i have three cell lines(HF,HT,NLT),treated on 3 time points > separately(1,4,12hrs). > I want to make comparison (HF vs HT),(HF vs NLT),(HT vs NLT). > I am using M value for comparison produced by limma after normalization. > I followed the given commands and i am stucked at this error given below. > > library(limma) > library(maSigPro) > data <- read.maimages(targets,source="agilent") >> MAW <- normalizeWithinArrays(data,method="loess",bc.method="subtract") >> edesign.abiotic <-read.table ("edesignabiotic.txt",header=TRUE) >> names(MAW) > [1] "targets" "genes" "source" "M" "A" >> data.abiotic<- MAW$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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.2 years ago by James W. MacDonald48k
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]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > 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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.2 years ago by neeraj rana60
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]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > -- > 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
ADD REPLYlink written 5.2 years ago by James W. MacDonald48k

$edesign
   Time Replicate Control X12hours_post_infection X24hours_post_infection X2days_post_infection
1     0         1       1                       0                       0                     0
2     0         2       1                       0                       0                     0
3     0         3       1                       0                       0                     0
4    12         1       0                       1                       0                     0
5    12         2       0                       1                       0                     0
6    12         3       0                       1                       0                     0
7    24         1       0                       0                       1                     0
8    24         2       0                       0                       1                     0
9    24         3       0                       0                       1                     0
10    2         1       0                       0                       0                     1
11    2         2       0                       0                       0                     1
 

 

ADD REPLYlink written 3 months ago by sbbinfo900
0
gravatar for sbbinfo90
3 months ago by
sbbinfo900
sbbinfo900 wrote:

Hello Jim,

I am also facing same problem. 

>fit <- p.vector(log_counts, design, Q = 0.05, MT.adjust = "BH", min.obs = 25)

Error in dat[, as.character(rownames(dis))] : subscript out of bounds

> head(log_counts)
           axenic_1  axenic_2  axenic_3  hpi12_1  hpi12_2  hpi12_3  hpi24_1  hpi24_2  hpi24_3   dpi2_1
UMAG_00001 11.00352  9.459432  9.350939 4.247928 4.321928 4.857981 4.459432 4.584963 4.643856 4.087463
UMAG_00002 11.65553 11.663558 11.904258 4.807355 5.044394 5.857981 4.700440 3.700440 4.247928 6.491853
             dpi2_2   dpi2_3    dpi4_1   dpi4_2   dpi4_3    dpi6_1    dpi6_2    dpi6_3    dpi8_1
UMAG_00001 4.247928 3.459432  4.087463 4.247928 4.754888  5.169925  5.554589  5.392317  5.169925
UMAG_00002 6.794416 6.209453  5.882643 5.832890 5.807355  7.076816  7.066089  7.129283  6.727920
              dpi8_2    dpi8_3   dpi12_1   dpi12_2   dpi12_3
UMAG_00001  5.832890  5.930737  6.672425  6.228819  7.139551
UMAG_00002  7.139551  6.554589  7.409391  6.870365  8.471675
 

ADD COMMENTlink written 3 months ago by sbbinfo900

$groups.vector
 [1] "X12hours_post_infectionvsControl" "X24hours_post_infectionvsControl"
 [3] "X2days_post_infectionvsControl"   "X4days_post_infectionvsControl"  
 [5] "X6days_post_infectionvsControl"   "X8days_post_infectionvsControl"  
                      
......[63]

ADD REPLYlink written 3 months ago by sbbinfo900
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