... The message you show looks good - this is exactly what you are supposed to see.
Now, you need to decide what package to use depending on the type of data you have and analysis you want to do.
... Your question is not clear to me. Could you clarify what you are trying to do and/or answer the following questions.
Are you replicating the example for raw MS data shown in the qcmetrics vignette, or are you creating you own QcMetric objects?
What is your input format, and what operability with ...
... What you see is a warning that highlights the version mismatch. In most cases, it can be ignored and everything will work as expected. In the past, when Rcpp had more substantial changes, error happened. If this happens, please report back. Otherwise, enjoy mzR and msPurity.
... 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