... The distribution certainly look weird, and it would be important to understand why they show such a conservative trend. Could it be that their have already been adjusted? This post is relevant.
Anyway, applying qvalue, or any adjustment, is not going to be of any help without first troubleshooting ...
... You need to update your version of R (current version is 3.4, you are still using 3.2), which will get you the latest version of DESeq2 (v 1.16.0, you have 1.10.1) and vst, which was introduced in version 1.12.0.
... The Cambridge Centre for Proteomics (CCP) is currently looking to recruit an experienced post-doctoral bioinformatician within its core facility unit.
The successful candidate will be required to analyse high-throughput proteomics datasets using numerous proteomic software packages (e.g. Proteome D ...
... The hyperLOPIT2015 data lives in the pRolocdata package, which you need to load first:
MSnSet (storageMode: lockedEnvironment)
assayData: 5032 features, 20 samples
element names: exprs
... From the data you show at the top, all proteins are down-regulated because the intensities in your controls are lower than in your treatment, hence negative log2 fold-changes.
If it is the negative values that confuse you, it is because down-regulation (i.e fold-changes between 0 and 1) become nega ...
... The only type of MS-based quantitation that is amenable to DESeq2 (or similar approaches) is spectral counting. Other approaches, whether labelled of unlabelled, are continuous data; I would also recommend limma for their analysis.
... I don't think the error you see is a linker issue. The problem is that the files that you want to read are cdf files
 "ko15.CDF" "ko16.CDF" "ko18.CDF" "ko19.CDF" "ko21.CDF" "ko22.CDF"
 "wt1 ...
... I am following up about this issue which has been resolved. Details available here.