search for: genespring

...ving trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R 3) Since I don't have LATEX for windows, I used texi2dvi from the CYGWIN package 4) When I run the command in Cygwin 'texi2dvi -c -p GeneSpring.tex' I get the error shown below. 5) When I edit the GeneSpri...

...ay (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the GeneSpring data analysis program (GeneSpring) TOOLS: ====== The released packages include tools which facilitate: * annotation * data management and organization through the use of the S4 class structure * identification of differentially expressed genes and clustering * quality assurance and cont...

Hi, I need some help with the interpretation of B statistics generated by eBayes in the limma package. I want to compare gene expression in three groups of Affy samples. The expression set has been imported from GeneSpring using GSload.expBC and a linear model fitted to the data using a design based on the three groups (6, 5, and 5 samples in each group, respectively). I have then made 3 contrasts to cover all possible comparisons within the data set, and generated empirical Bayes statistics using eBayes. I'v...

Sorry i had a misprint in the appendix code in the last email Hi I needed some help with ANOVA I have a problem with My ANOVA analysis. I have a dataset with a known ANOVA p-value, however I can not seem to re-create it in R. I have created a list (zzzanova) which contains 1)Intensity Values 2)Group Number (6 Different Groups) 3)Sample Number (54 different samples) this is created by the