Dear Friends, We make use Agilent scanner and feature extraction software for TIFF (16 bit) image extraction. But I have some doubts on the Feature extraction output. In output, I find all intensity values (example: log ratio, rProcessedSignal, gProcessedSignal, gMeanSignal, rMeanSignal etc) are given in log base 10. Now my question is, 1. Whether it is common to measure microarray binary data (TIFF) in log base 10 or log base 2? 2. In case, measuring microarray intensities in log base 10 is right, how come LIMMA will come to know that, intensity values are in log base 10? How does it calculates M and A value in log base 2? I request any of you to answer my question. Thanking you in anticipation. Regards, Prashantha ###################################################################### Attention:\ This e-mail message is privileged and confid...{{dropped:10}}

Hi, Prashantha Hebbar wrote: > We make use Agilent scanner and feature extraction software for TIFF (16 > bit) image extraction. But I have some doubts on the Feature extraction > output. In output, I find all intensity values (example: log ratio, > rProcessedSignal, gProcessedSignal, gMeanSignal, rMeanSignal etc) are given > in log base 10. Now my question is, > > 1. Whether it is common to measure microarray binary data (TIFF) in > log base 10 or log base 2? I suppose you are right that in the microarray community, everybody seems to use binary logarithms (log2). Bear in mind, however, that this is rather uncommon in other fields: most physicists and electrical engineers prefer to work with decimal logarithms (log10). Maybe the read-out software has been written by someone working outside of molecular biology. > 2. In case, measuring microarray intensities in log base 10 is right, > how come LIMMA will come to know that, intensity values are in log base 10? > How does it calculates M and A value in log base 2? My guess would be that LIMMA won't notice. But as you know, log10 and log2 values are proportional, and as LIMMA works with t values, which are ratios of log-scales quantities, the conversion factor between log10 and log2 will cancel out and won't affect your p values. Still, you could simply divide everything by log10( 2 ) to convert from log10 to log2. HTH Simon +--- | Dr. Simon Anders, Dipl. Phys. | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK