Reading the NCBI’s GEO microarray SOFT files in R/BioConductor

This page discusses how to load GEO SOFT format microarray data from the Gene Expression Omnibus database (GEO) (hosted by the NCBI) into R/BioConductor. SOFT stands for Simple Omnibus Format in Text. There are actually four types of GEO SOFT file available:

GEO Platform (GPL) These files describe a particular type of microarray. They […]


Meta分析的由来: Meta分析(Meta-analysis)是心理学家Glass于1976年首次提出,原文是这样的: Meta-analysis refers to the analysis of analyses. I use it to refer to the statistical analysis of a large collection of results from individual studies for the purpose of integrating the findings. It connotes a rigorous alternative to the casual, narrative discussions of research studies which typify our attempts to make sense of […]

MrBayes Tree

Use clustalw to generate nexus format file

#NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format missing=? symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ” interleave datatype=DNA gap= -;

Change to as follows: #NEXUS BEGIN DATA; dimensions ntax=55 nchar=534; format datatype=dna interleave=yes gap=- missing=?;

then type mb -i *.nex

MrBayes > lset nst=6 rates=invgamma

Setting Nst to 6 Setting Rates to Invgamma Successfully […]