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Question: VirtualArray
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gravatar for Michael Breen
4.1 years ago by
Michael Breen350
Michael Breen350 wrote:
Hi all, We are interested in using VirtualArray while mining a few datasets into order to ask more theoretical questions than the data was originally intended for. However, to set the foundation I need to merge various data-sets from very similar platforms. I have just a couple questions regarding the application of VirtualArray. To reduce complexity in our dialogue I will just refer to 2 GEO datasets for the time being. First, we have checked the expression summaries of each of the GeoSets. How does your program infer which normalizing to perform on one data-set vs. the other to make the distributions more similar to each other? I can make assumptions with the below example, however do you have a test for this? > summary(Eset1)[,1:3] Pat1 Pat2 Pat3 "Min. :-1.48434 " "Min. :-1.628659 " "Min. :-1.63216 " "1st Qu.:-0.05553 " "1st Qu.:-0.075109 " "1st Qu.:-0.08433 " "Median : 0.01388 " "Median :-0.001093 " "Median : 0.02052 " "Mean : 0.01210 " "Mean : 0.002367 " "Mean : 0.02474 " "3rd Qu.: 0.10731 " "3rd Qu.: 0.075719 " "3rd Qu.: 0.16198 " "Max. : 2.01628 " "Max. : 2.439713 " "Max. : 1.62180 " > summary(Eset2)[,1:3] Pat1 Pat2 Pat3 "Min. : 0.8523 " "Min. : 0.8373 " "Min. : 0.6775 " "1st Qu.: 4.6027 " "1st Qu.: 4.4968 " "1st Qu.: 4.4723 " "Median : 6.0780 " "Median : 6.0009 " "Median : 5.9944 " "Mean : 6.1098 " "Mean : 6.0757 " "Mean : 6.0891 " "3rd Qu.: 7.4339 " "3rd Qu.: 7.4802 " "3rd Qu.: 7.5196 " "Max. :13.5664 " "Max. :13.4372 " "Max. :13.3803 " Second, when compiling the new expression set with: > my_virtualArrays$iPSC_hESC_noBatchEffect <- virtualArrayExpressionSets() While this runs we have run into 2 problems. The first being that our annotation type is GPL5175 for both Esets in this example. And we will receive the following error: Error in eval(expr, envir, enclos) : object 'GPL5175SYMBOL' not found. The second is that this step also relies upon the BiocParallel bioconductor source package which does not seem to be installing for R v. 3.0.2. I have attempted bioconductor download, install.packages command, reinstallation of R etc... with no advances. Any insight to the above questions would be great. Yours, Michael [[alternative HTML version deleted]]
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4.1 years ago by
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