James MacDonald
2004-Jul-13 16:12 UTC
[R] Difference between normalizeWithinArrays and stat.ma
Since both of the packages you mention are part of Bioconductor, you would do well to re-post in the correct list (bioconductor at stat.math.ethz.ch). Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623>>> "Saroj Mohapatra" <saroj at wayne.edu> 07/13/04 01:51PM >>>Dear friends I have recently migrated to R (8.0) for analysis of microarray data. I am doing a loess (print-tip, perhaps scaled) normalization. I find that there are 2 options to do this: using normalizeWithinArrays (Limma) and stat.ma(sma). I find the objects returned by the two functions are different, however the M and A values seem to be the same. Is one function preferable over the other? Any feedback regarding this would be appreciated. Thanks and regards, Saroj -------------------------- Saroj K Mohapatra, MD Research Associate Karmanos Cancer Institute Wayne State University School of Medicine 110 E. Warren, Room 311 Detroit MI 48201 313-833-0715 x2424 saroj at wayne.edu ______________________________________________ R-help at stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Saroj Mohapatra
2004-Jul-13 17:51 UTC
[R] Difference between normalizeWithinArrays and stat.ma
Dear friends I have recently migrated to R (8.0) for analysis of microarray data. I am doing a loess (print-tip, perhaps scaled) normalization. I find that there are 2 options to do this: using normalizeWithinArrays (Limma) and stat.ma(sma). I find the objects returned by the two functions are different, however the M and A values seem to be the same. Is one function preferable over the other? Any feedback regarding this would be appreciated. Thanks and regards, Saroj -------------------------- Saroj K Mohapatra, MD Research Associate Karmanos Cancer Institute Wayne State University School of Medicine 110 E. Warren, Room 311 Detroit MI 48201 313-833-0715 x2424 saroj at wayne.edu
Saroj Mohapatra
2004-Jul-13 19:39 UTC
[R] Difference between normalizeWithinArrays and stat.ma
Dear friends I have recently migrated to R (8.0) for analysis of microarray data. I am doing a loess (print-tip, perhaps scaled) normalization. I find that there are 2 options to do this: using normalizeWithinArrays (Limma) and stat.ma(sma). I find the objects returned by the two functions are different, however the M and A values seem to be the same. Is one function preferable over the other? Any feedback regarding this would be appreciated. Thanks and regards, Saroj -------------------------- Saroj K Mohapatra, MD Research Associate Karmanos Cancer Institute Wayne State University School of Medicine 110 E. Warren, Room 311 Detroit MI 48201 313-833-0715 x2424 saroj at wayne.edu