Question: affycoretools vennSelect problem
0
gravatar for PeadarÓGaora
11.1 years ago by
PeadarÓGaora30 wrote:
Hello BioCer's, I've been using affycoretools, particularly limma2annaffy,for a while now and love it. These wrappers really make life simpler. However (there was bound to be a however), in a recent experiment I've had some problems with vennSelect. The experiment has 4 groups and 4 time points, 5 replicates each. There are then, a plethora of possible contrasts of interest. I've run one particular analysis with 34 contrasts and wanted to look at the unique (differentially expressed, p<0.05) genes and intersections between some of them. When I use vennSelect to do this, it returns probesets with P values well above 0.05. I can't see where it is picking these from as the lists from the individual contrasts all look perfectly fine (P-value for all selected genes < 0.05). I have tried subsetting the TestResults and contrasts matrices in the call to vennSelect. I've also tried generating new ones TestResults objext and contrast matrix which include only the comparisons being analysed. The fit object however contains the entire dataset. Could this be where things are going wrong? Any help much appreciated. Peadar > sessionInfo() R version 2.5.1 (2007-06-27) ia64-unknown-linux-gnu locale: LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE .UTF-8;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" [7] "utils" "methods" "base" other attached packages: affycoretools annaffy xtable gcrma matchprobes "1.8.1" "1.8.1" "1.5-1" "2.8.1" "1.8.1" biomaRt RCurl XML GOstats Category "1.10.1" "0.8-0" "1.92-1" "2.2.6" "2.2.3" Matrix lattice genefilter survival KEGG "0.999375-2" "0.15-11" "1.14.1" "2.32" "1.16.1" RBGL annotate GO graph limma "1.12.0" "1.14.1" "1.16.0" "1.14.2" "2.10.5" affy affyio Biobase "1.14.2" "1.4.1" "1.14.1" -- ############################ Dr. Peadar ? Gaora UCD Conway Institute, Belfield, Dublin 4. (01) 716-6915 ############################
ADD COMMENTlink modified 11.1 years ago by James W. MacDonald50k • written 11.1 years ago by PeadarÓGaora30
Answer: affycoretools vennSelect problem
0
gravatar for James W. MacDonald
11.1 years ago by
United States
James W. MacDonald50k wrote:
Hi Peadar, Peadar ? Gaora wrote: > Hello BioCer's, > > I've been using affycoretools, particularly limma2annaffy,for a while > now and love it. These wrappers really make life simpler. > > However (there was bound to be a however), in a recent experiment I've > had some problems with vennSelect. The experiment has 4 groups and 4 > time points, 5 replicates each. There are then, a plethora of possible > contrasts of interest. I've run one particular analysis with 34 > contrasts and wanted to look at the unique (differentially expressed, > p<0.05) genes and intersections between some of them. When I use > vennSelect to do this, it returns probesets with P values well above > 0.05. If you have more than three contrasts, vennSelect() is supposed to error out with a message - is that not happening? > > I can't see where it is picking these from as the lists from the > individual contrasts all look perfectly fine (P-value for all selected > genes < 0.05). I have tried subsetting the TestResults and contrasts > matrices in the call to vennSelect. I've also tried generating new ones > TestResults objext and contrast matrix which include only the > comparisons being analysed. The fit object however contains the entire > dataset. Could this be where things are going wrong? I haven't made many changes to affycoretools for a while, but that version of R/BioC is seriously ancient. The first step should be to upgrade to R-2.7.1 and BioC 2.2. Then you should show the code you are using (hopefully simplified if possible). Best, Jim > > > Any help much appreciated. > > Peadar > > >> sessionInfo() > R version 2.5.1 (2007-06-27) > ia64-unknown-linux-gnu > > locale: > LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_ IE.UTF-8;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_I E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" > "datasets" > [7] "utils" "methods" "base" > > other attached packages: > affycoretools annaffy xtable gcrma matchprobes > "1.8.1" "1.8.1" "1.5-1" "2.8.1" "1.8.1" > biomaRt RCurl XML GOstats Category > "1.10.1" "0.8-0" "1.92-1" "2.2.6" "2.2.3" > Matrix lattice genefilter survival KEGG > "0.999375-2" "0.15-11" "1.14.1" "2.32" "1.16.1" > RBGL annotate GO graph limma > "1.12.0" "1.14.1" "1.16.0" "1.14.2" "2.10.5" > affy affyio Biobase > "1.14.2" "1.4.1" "1.14.1" > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 11.1 years ago by James W. MacDonald50k
Hi Jim, Thanks for getting back to me. On Mon, 2008-06-23 at 09:18 -0400, James W. MacDonald wrote: > Hi Peadar, > > Peadar ? Gaora wrote: > > Hello BioCer's, > > > > I've been using affycoretools, particularly limma2annaffy,for a while > > now and love it. These wrappers really make life simpler. > > > > However (there was bound to be a however), in a recent experiment I've > > had some problems with vennSelect. The experiment has 4 groups and 4 > > time points, 5 replicates each. There are then, a plethora of possible > > contrasts of interest. I've run one particular analysis with 34 > > contrasts and wanted to look at the unique (differentially expressed, > > p<0.05) genes and intersections between some of them. When I use > > vennSelect to do this, it returns probesets with P values well above > > 0.05. > > If you have more than three contrasts, vennSelect() is supposed to error > out with a message - is that not happening? vennSelect behaves exactly that way if I feed it more than 3 contrasts. What I've been doing is subsetting the TestResults and contrast matrix to the two contrasts I want to look at eg: vennSelect(gcrma_Data, design, interday_res[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday.contrasts[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday_fit2, stat="tstat") where pregHi_d5vd7 and pregLo_d5vd7 are contrasts of interest. Having written this, I've just found that the problem was indeed passing in the entire fit object. Subsetting this as well corrects the issue. I had tried and failed to do that before but I guess I had a typo in the command. Anyway, I just thought I should finish this out in case anybody checking the archives in the future has a similar question. so the correct call should have been: vennSelect(gcrma_Data, design, interday_res[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday.contrasts[,c("pregHi_d5vd7", "pregLo_d5vd7")],interday_fit2[,c("pregHi_d5vd7", "pregLo_d5vd7")], stat="tstat") Go raibh m?le maith agat Jim, Peadar > > > > > I can't see where it is picking these from as the lists from the > > individual contrasts all look perfectly fine (P-value for all selected > > genes < 0.05). I have tried subsetting the TestResults and contrasts > > matrices in the call to vennSelect. I've also tried generating new ones > > TestResults objext and contrast matrix which include only the > > comparisons being analysed. The fit object however contains the entire > > dataset. Could this be where things are going wrong? > > I haven't made many changes to affycoretools for a while, but that > version of R/BioC is seriously ancient. The first step should be to > upgrade to R-2.7.1 and BioC 2.2. > Then you should show the code you are using (hopefully simplified if > possible). > > Best, > > Jim > > > > > > > > > Any help much appreciated. > > > > Peadar > > > > > >> sessionInfo() > > R version 2.5.1 (2007-06-27) > > ia64-unknown-linux-gnu > > > > locale: > > LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=e n_IE.UTF-8;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en _IE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.U TF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" > > "datasets" > > [7] "utils" "methods" "base" > > > > other attached packages: > > affycoretools annaffy xtable gcrma matchprobes > > "1.8.1" "1.8.1" "1.5-1" "2.8.1" "1.8.1" > > biomaRt RCurl XML GOstats Category > > "1.10.1" "0.8-0" "1.92-1" "2.2.6" "2.2.3" > > Matrix lattice genefilter survival KEGG > > "0.999375-2" "0.15-11" "1.14.1" "2.32" "1.16.1" > > RBGL annotate GO graph limma > > "1.12.0" "1.14.1" "1.16.0" "1.14.2" "2.10.5" > > affy affyio Biobase > > "1.14.2" "1.4.1" "1.14.1" > > >
ADD REPLYlink written 11.1 years ago by PeadarÓGaora30
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