Category Archives: Keiko

PC-ORD:nMDS and R:heatmaps

PC-ORD Non-metric Multidimensional Scaling and Correlations Imported Main Matrix “MM” sheet from “PCORD_only_Base.xlsx” Imported Environmental “EM” sheet from “PCORD_only_Base.xlsx” Ran analysis: Ordination|NMS|autopilot/Slow & thorough Took about 20 min. No option to “Graph Ordination”. Graphed NMS Scree Plot. Not exactly sure … Continue reading

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Meeting with Dr. Lamendella #2

Things we figured out metadata ID names are some combination of RS number, visit etc. separated by dots. metadata after baseline is on computer at Lamendella’s house. Should receive by end of the day. Things we need to do for … Continue reading

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Getting Acquainted with Data/QIIME interface

Andrew and I met at approximate 9:27PM to start exploring the QIIME online interface and get a better feel of the data that is generated by QIIME (http://www.microbio.me/qiime/). We were able to download a .jnlp file after doing a test … Continue reading

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Meeting with Dr. Lamendella

Goals Determined location of OTU table. Meta analysis>input name>perform analysis>find “dietary crossover” TO DO: Add data after baseline. Upload metadata, format into qiime. Search qiime database to learn how to deal with database How to convert .biome file to .xls … Continue reading

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Tutorial for QIIME

http://qiime.org/tutorials/tutorial.html This tutorial explains how to use the QIIME (Quantitative Insights Into Microbial Ecology) Pipeline to process data from high-throughput 16S rRNA sequencing studies. If you have not already installed qiime, please see the section Installing Qiime first. The purpose of this pipeline is … Continue reading

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First meeting

Attempted to install VirtualBox and QIIME, but need adminstrative access. Set up blog to keep track of shit, literally. Currently attempting to install VirtualBox on Keiko’s laptop. Goals this weekend: Find articles, tutorials on QIIME, set up meeting with Lamendella, … Continue reading

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