Martin Stoffel

10 Questions 23 Answers 0 Followers

Questions related from Martin Stoffel

Can anyone recommend a service provider for library preparation and 16s sequencing of bacterial samples from animals?

For my project, I want to analyse the bacterial community composition of anal swabs from seals. Thus, I'm searching a reliable service provider for both the library preparation as well as 16s...

11 November 2017 6,489 2 View

How do I convert a SNP genotype table into plink binary PED files?

My raw data is simple: One column of SNP IDs followed by two columns for each locus where 1 is allel A and 2 is allel B. A homozogote would thus have 1 1 or 2 2 in the two first columns and a...

02 February 2015 9,632 14 View

How to calculate the explained variance per factor in a principal axis factor analysis?

I did a principal axis factor analysis with promax (oblique) rotation in R. Now I want to compute the explained variance for all factors of my 4-factor solution. I can extract the eigenvalues but...

11 November 2014 7,957 10 View

What's the best model to predict a categorical outcome with 41 levels (in R)?

Precisely, I want to find out which of the 4 variables can predict membership to the 41 groups (each consisting of just 2 observations).

09 September 2014 8,200 8 View

Can anyone help with R pipeline to calculate Fst measure of population differentiation from AB1 files?

I am a real beginner in bioinformatics and need some hints. My data are mtDNA sequences in the AB1 format. My aim is to compute the Fst to get some insights in the population differentiation...

08 August 2014 6,685 5 View

Why run a Mantel test instead of a glm? What about multiple testing?

I am currently doing an analysis where I have to do multiple Mantel tests. Concerning the problem of multiple Testing I am thinking of "rolling out" the matrices to vectors and then just do a GLM....

07 July 2014 1,691 3 View

Can anyone suggest a good overview article for the ecology of olfaction?

Especially concerning communication, kin recognition, mate choice?

07 July 2014 554 4 View

How can I do Factor Analysis / PCA with more variables than observations in R?

I´ve got a data set with 82 observations and 220 variables. What I want to do is basically a PCA but with varimax and maybe even oblique rotation of the resulting factors as I want to look for an...

07 July 2014 4,959 13 View

How many principal components can I extract from a PCA?

I'm working on seal olfaction and did a PCA on a matrix of 220 scent compounds from 82 individuals. Is there a good way to figure out how many PCs may be relevant? I already did a scree plot and...

06 June 2014 8,019 14 View

What is the best method to align chromatograms/peaks from GCMS?

The chromatograms are saved as Xcalibur files and i want to align them (e.g. via R). They actually have a large variance in peak number / concentration and i need an algorithm to make them...

02 February 2014 3,175 17 View