Hello,

I am doing an RNA-seq data analysis. I already have several spesific gene as my target. What I want to do is actually comparing the gene expression level with the SNP mutation. So, for now, I want to get the gene expression level with this RNA-seq data. Because of my analysis focus on SNP and gene expression analysis, I don' have any interest in between group differential expression analysis. I already follow DESeq2 tutorial but I only get the fold change difference for 2 groups, normal and disease. So, the question is, I want to check the fold change to 1 of the sample as the base. I imagine like this. I have 14 sample. I will have fold change for difference between 1 and 2, 1 and 3, and so on, until 1 and 14. So, is this method possible to do in DESeq2 and probably you can share your idea how to do this with DESeq2. Thank you very much for your help. 

Using one sample as a baseline is not a good idea. Check the manual on using single samples in dispersion estimation. What you could do, is if this is a SNP for a particular gene, you could get the normalised counts and look at that particular gene entry? 

counts(dds,normalized=TRUE)

Is "calculating fold changes" really what you want?

If so, just use

nc <- counts( dds, normalized=TRUE )

to obtain a matrix of normalized counts. Now, if you write

nc[,3]/nc[,1]

then you get a vector with fold changes of sample 3 vs sample 1. Of course, DESeq also offers what we call "shrunken log fold changes", which are log fold changes that are biased towards zero for noisy genes. (See vignette and paper for details.) For this, use "rlogTransformation" instead of "counts" (and use "-" instead of "/" because it is on the log scale).
 

Somehow, though, I feel that you might need more than though for your problem.

And the question you wanted to ask was not "how to calculate fold changes between specific samples?", but "How to perform a standard eQTL analysis on RNA-Seq data in R/Bioconductor?"

I guess one answer to that would be to use DESeq2's rlogTransformation to get a data matrix to feed to the GGTool package, but maybe somebody else here has a more up-to-date answer. (I have little hands-on experience with this.)