From a statistical viewpoint it is the best is to record both, the "nondetect" value (e.g. < 0.01) and the original measurement, even if it is below the detection limit (and even if it is negative!), see:

Analytical Methods Committee (2001) Measurement of near zero concentration: recording and reporting results that fall below the detection limit. The Analyst 126, 256-259.

See also: Analytical Methods Committee (2001) What should be done with results below the detection limit? Mentioning the unmentionable. Royal Society of Chemistry, amc technical brief. http://www.rsc.org/images/results-below-detection-limit-technical-brief-5_tcm18-214854.pdf

If there is no chance to get the original value, it is not that easy, but you may try to estimate the distribution of these values. The R package NADA (Nondetects And Data Analysis for environmental data) from the USGS supports this:

http://cran.r-project.org/package=NADA

The background can be found in a related book: Helsel, D. (2004) Nondetects and Data Analysis: Statistics for Censored Environmental Data (Statistics in Practice). Wiley-Interscience, 268pp.

Finally, an overview about the methods was presented by the book and package authors at the useR! conference in Dortmund 2004, the slides are still online: http://www.statistik.uni-dortmund.de/useR-2008/slides/Helsel+Lee.pdf

Hope it helps,

Thomas

Helsel also has a newer book "Statistics for Censored Environmental Data Using Minitab(R) and R" (2012) which provides a good summary of different ways to record and include censored data in statistical analyses.

hi thomas, thanks for your information, i will try to learn your suggestion

here the same document talking about NADA for R package

http://www.practicalstats.com/nada/downloads_files/NADAforR_Examples.pdf

Please see my papers:

Article Non-Gaussian Covariate-Dependent Spatial Measurement Error M...

and

Article Bayesian Analysis of Skew Gaussian Spatial Models Based on C...

USGS has a publication that would be helpful in answering your question.

Techniques of Water-Resource Investigations of the USGS Book 4 Hydrologic Analysis and interpretations. Chapter A3 Statistical Methods in Water Resources.

https://pubs.usgs.gov/twri/twri4a3/pdf/twri4a3-new.pdf

Chapter 13 in the above publication should answer your questions "Methods for Data Below the Reporting Limit." Direct link to Chapter 13 is below. https://pubs.usgs.gov/twri/twri4a3/pdf/chapter13.pdf