ArrayAssist vs. Bioconductor
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@groot-philip-de-1307
Last seen 8.4 years ago
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@bogdan-georgescu-1432
Last seen 8.4 years ago
Hello, We have confirmed that all algorithm steps involved in both RMA and GC-RMA are identical between the Bioconductor packages and ArrayAssist 3.3. As some people have suggested before in this thread, the differences in outcome arise solely as a result of implementation choices--sometimes Bioconductor packages will employ routines coded in R, where ArrayAssist uses high-performance C++ libraries and native C/C++ and Fortran code. We have performed extensive comparative analysis of all final and partial results from Bioconductor and ArrayAssist implementations of the algorithms in question. The analysis confirmed that the issues are limited to implementation differences. Algorithm steps coded using the same language produced identical results in both environments. Algorithm steps coded using different languages (and converted to executable code using different compilers) produced slightly different results. Practically, the differences are limited to the calculation of loess coefficients for background estimation. We are consistently obtaining correlation values between Bioconductor and ArrayAssist in excess of 0.99, often better than 0.9999. Please note that different data sets will produce different results due to varying data distribution and to the probabilistic component involved in the calculations. Bogdan Georgescu Stratagene Software Solutions PS. Philip, the latest version of ArrayAssist may be downloaded using the Check for Updates feature. The corrections you mention are all in version 3.3.
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