bmbolstad.com

Ben Bolstad Webpage

University Of California, Berkeley. I have been heavily involved with the development of statistical algorithms for microarray data analysis. Including spending a great deal of time as a member of Terry Speed's group. I developed the Quantile Normalization. Contains a number of images demonstrating the results of these techniques. In 2005 I spent time at Predicant Biosciences. Developing statistical and computational techinques for the analysis of mass spectrometry data.

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Ben Bolstad Webpage | bmbolstad.com Reviews

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University Of California, Berkeley. I have been heavily involved with the development of statistical algorithms for microarray data analysis. Including spending a great deal of time as a member of Terry Speed's group. I developed the Quantile Normalization. Contains a number of images demonstrating the results of these techniques. In 2005 I spent time at Predicant Biosciences. Developing statistical and computational techinques for the analysis of mass spectrometry data.

<META> KEYWORDS

1 ben bolstad

2 publications

3 software

4 talks/posters

5 teaching

6 misc

7 biostatistics

8 email bmb@bmbolstad com

9 research

10 at uc berkeley

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Ben Bolstad Webpage | bmbolstad.com Reviews

https://bmbolstad.com

University Of California, Berkeley. I have been heavily involved with the development of statistical algorithms for microarray data analysis. Including spending a great deal of time as a member of Terry Speed's group. I developed the Quantile Normalization. Contains a number of images demonstrating the results of these techniques. In 2005 I spent time at Predicant Biosciences. Developing statistical and computational techinques for the analysis of mass spectrometry data.

SUBDOMAINS

plmimagegallery.bmbolstad.com

PLM Image Hall of Fame

Maintained by Ben Bolstad. The goal of this website is to show some of the interesting artifacts observed in the chip pseudo-images produced by the PLM procedures in the BioConductor. AffyPLM package or via RMAExpress. Script. Please email me for more details on what you should submit bmb@bmbolstad.com. You can read more about how to use affyPLM from BioConductor. To produce similar images in:. Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S. (Eds.), Springer, 2005. Publisher Website.

math124sfsu.bmbolstad.com

SFSU MATH 124 Class page

SFSU Math 124 - Elementary Statistics Spring 2005. Instructor: Dr Ben Bolstad. Email: bolstad math124@bmbolstad.com. Office Hours: 11-12pm Tuesday and Thursday (or by appointment). Syllabus and other important notices. Syllabus and Course Outline. Message for all mathematics students from chair. Publishers supplementary website for the textbook. How to Load Data from tab delimitted text file. How to Draw a Histogram. How to Draw a Boxplot. How to Compute Summary Statistics. How to Draw a Scatterplot.

math324sfsu.bmbolstad.com

SFSU MATH 324 Class page

SFSU Math 324 - Probability and Statistics with Computing Fall 2004. Instructor: Dr Ben Bolstad. Email: bolstad math324@bmbolstad.com. Office Hours: 1-2pm Monday and Wednesday. Syllabus and other important notices. Syllabus and Course Outline. Message for all mathematics students from chair. Handouts and Computer code. Computing guide: Getting Started. Computing guide: Introduction to R. Computing guide: Introduction to Minitab. R code useful for Assignment 2. Some Minitab useful for Assignment 2. CH 3: ...

rmaexpress.bmbolstad.com

RMAExpress

Written by Ben Bolstad. RMAExpress is a standalone GUI program for Windows, OS X and Linux to compute gene expression summary values for Affymetrix Genechip data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R. Nor is it dependent on any component of the BioConductor. Project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays. Accepted for publication in Biostatistics. [ Abstract. Should be...

INTERNAL PAGES

bmbolstad.com

1

Supplementary information for Bolstad et al (2003) Normalization of Oligonucleotide arrays

http://www.bmbolstad.com/misc/normalize/normalize.html

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003). A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. 19,2,pp 185-193. Astrand, Magnus (2001) Normalizing Oligonucleotide Arrays. Bolstad, B (2001) Probe Level Quantile Normalization for High Density Oligonucleotide Array Data Unpublished Manuscript. All figures in manuscript Figures.tar.gz. Figure 1 Fig1.png. Figure 2 Fig2.png. Figure 3 Fig3.png. Figure 4 Fig4.png. Demonstration o...

2

Ben Bolstad Software

http://www.bmbolstad.com/software.html

I have written an number of pieces of software. Mostly for the analysis of microarray data. For more information see my software. Page I am currently a BioConductor contributor. Some notes/FAQ on the software. Why do my MAS 5.0 values differ? Explains the differences between the MAS 5.0 implementation in BioConductor affy. Package and those that you might get from Affymetrix MAS 5.0 software. Some FAQ about computing the RMA expression measure.

3

Ben Bolstad Publications

http://www.bmbolstad.com/publications.html

2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Dissertation. University of California, Berkeley. Postscript. These are some of the articles I have been involved with:. Sandrine Dudoit,Yee Hwa Yang and Ben Bolstad. 2002) Using R for the Analysis of DNA Microarray Data, R News, 2, 1, 24-32 Rnews. Bolstad, B.M. Note that this paper was named a hot paper. By ISI Essential Science Indicators. Rafael. A. Irizarry, Benjamin M. Bolstad. Dettling ...

4

Ben Bolstad Software

http://www.bmbolstad.com/teaching.html

This is material for classes that I taught previously. It is left here for historical interest. I am not involved in any teaching activities at the current time. SFSU Math 124 Spring 2005. SFSU Math 124 Fall 2004. SFSU Math 324 Fall 2004. UCB Stat 215b Spring 2004 Section page. UCB Stat 20 Fall 2003 Section page. UCB STAT 200B (Spring '00) webpage. UCB STAT 200B (Spring '99) webpage.

5

Ben Bolstad Misc

http://www.bmbolstad.com/misc.html

To eat near the UC Berkeley Campus (From 2001ish era so many of these places no longer exist).

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plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/AffymetrixU95AAssessments/index.html

Affy U95A Spikein Assessment plots. May 2, 2004. FitPLM with default background and normalization. Comments From the Submitter:. These are other assessment plots. Weights and Residuals pseudo-chip images. Note that if you use the images for personal use on this page you should cite this website. In cases where the contributor is named please get permission directly from the contributor. Permission is not given for formal publications.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/AffymetrixU95ASpikeins/index.html

Affy U95A Spikein Complete Dataset. May 2, 2004. FitPLM with default background and normalization. Comments From the Submitter:. This is the entire Affymetrix U95A array dataset. Most arrays show no serious artifacts. Note that if you use the images for personal use on this page you should cite this website. In cases where the contributor is named please get permission directly from the contributor. Permission is not given for formal publications.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/RatDatasetAssessments/index.html

Rat Dataset Assessment Plots. June 7, 2004. FitPLM with default background and normalization. Comments From the Maintainer:. Weights and Residuals pseudo-chip images. Note that if you use the images for personal use on this page you should cite this website. In cases where the contributor is named please get permission directly from the contributor. Permission is not given for formal publications.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/E2A-PBX1/index.html

May 7, 2004. FitPLM with default background and normalization. Comments From the Submitter:. These are the E2A-PBX1 chips from a large public dataset:. Cancer Cell, 1, pp 133-143. Supplementary Data from Yeoh et al. Note that if you use the images for personal use on this page you should cite this website. In cases where the contributor is named please get permission directly from the contributor. Permission is not given for formal publications.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/StJudeALL2/index.html

St Jude ALL Dataset 2 Chips. June 2, 2005 (Updated Jul 11, 2005). RMAExpress version 0.4 alpha 5. Comments From the Submitter:. These are all the chips from a large public dataset:. Meyling H. Cheok, Wenjian Yang, Ching Hon Pui, James R. Downing, CHeng Cheng, Clayton W. Naeve, Mary V. Relling, William E. Evans Treatment-specific Changes in Gene Expression Discriminate in vivo Drug response in Human Leukemia Cells. Supplementary Data from Cheok et al. To download a zip archive containing fullsize images.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/StJudeALL1/index.html

St Jude ALL Dataset 1 Chips. May 25, 2005 (Updated Jul 12, 2005). RMAExpress version 0.4 alpha 5. Comments From the Submitter:. These are all the chips from a large public dataset:. Cancer Cell, 1, pp 133-143. Supplementary Data from Yeoh et al. To download a zip archive containing fullsize images.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/RatDataset/index.html

June 7, 2004. FitPLM with default background and normalization. Comments From the Maintainer:. I believe this dataset is representative of many small lab experiments. Many of the arrays have small artifacts, but in general the arrays have about equivalent quality relative to each other. Ben Bolstad.

plmimagegallery.bmbolstad.com

Contributed PLM Image

http://plmimagegallery.bmbolstad.com/E2A-PBX1Assessments/index.html

May 7, 2004. FitPLM with default background and normalization. Comments From the Submitter:. These are the E2A-PBX1 chips from a large public dataset:. Cancer Cell, 1, pp 133-143. Supplementary Data from Yeoh et al. Weights and Residuals pseudo-chip images. Note that if you use the images for personal use on this page you should cite this website. In cases where the contributor is named please get permission directly from the contributor. Permission is not given for formal publications.

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Ben Bolstad Webpage

University Of California, Berkeley. I have been heavily involved with the development of statistical algorithms for microarray data analysis. Including spending a great deal of time as a member of Terry Speed's group. I developed the Quantile Normalization. Contains a number of images demonstrating the results of these techniques. In 2005 I spent time at Predicant Biosciences. Developing statistical and computational techinques for the analysis of mass spectrometry data.

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