## ---- echo = FALSE, message = FALSE-------------------------------------- if (!require(msqc1)){ ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("msqc1") } ## ------------------------------------------------------------------------ msqc1:::.normalize_rt ## ------------------------------------------------------------------------ msqc1:::.reshape_rt ## ------------------------------------------------------------------------ msqc1:::.plot_rt_8rep msqc1:::.plot_rt_dil ## ----echo=TRUE, fig.width=8, fig.height=8, fig.retina=3, warning=FALSE, cache=FALSE, fig.asp=1, fig.cap=''---- S.training.8rep <- msqc1:::.reshape_rt(msqc1_8rep, peptides=peptides, cex=2) ## ----echo=TRUE, fig.width=15, fig.height=9, fig.retina=3, warning=FALSE, fig.cap='', cache=FALSE---- msqc1:::.plot_rt_8rep(msqc1_8rep, peptides=peptides, xlab='Replicate Id') ## ----echo=TRUE, fig.width=15, fig.height=9, fig.retina=3, warning=FALSE, cache=FALSE---- msqc1_8rep.norm <- msqc1:::.normalize_rt(msqc1_8rep, S.training.8rep, reference_instrument = 'Retention.Time.QTRAP') msqc1:::.plot_rt_8rep(msqc1_8rep.norm, peptides=peptides, xlab='Replicate Id', ylab='Normalized Retention Time') ## ----echo=TRUE, fig.width=8, fig.height=8, fig.retina=3, warning=FALSE, cache=FALSE, fig.asp=1, fig.cap=''---- S.training.dil <- msqc1:::.reshape_rt(msqc1_dil, peptides=peptides, cex=2) ## ----echo=TRUE, fig.width=15, fig.height=9, fig.retina=3, warning=FALSE, cache=FALSE---- msqc1:::.plot_rt_dil(msqc1_dil, peptides, xlab='Replicate Id', ylab='Raw Retention Time') msqc1_dil.norm <- msqc1:::.normalize_rt(msqc1_dil, S.training.dil, reference_instrument = 'Retention.Time.QTRAP') msqc1:::.plot_rt_dil(msqc1_dil.norm, peptides=peptides, ylab="Normalized Retention Time") ## ----echo=FALSE, fig.width=10, fig.height=5, fig.retina=3, warning=FALSE, cache=FALSE---- op <- par(mfrow=c(1,2), mar=c(4,4,1,1)) plot(msqc1_8rep.norm$Retention.Time ~ msqc1_8rep$Retention.Time, pch=as.integer(msqc1_8rep.norm$Peptide.Sequence), col=msqc1_8rep.norm$instrument, xlim=c(0,100)) legend("bottomright", as.character(unique(msqc1_8rep.norm$instrument)), col= unique(msqc1_8rep.norm$instrument), pch=as.integer(unique(msqc1_8rep.norm$instrument))) plot(msqc1_dil.norm$Retention.Time ~ msqc1_dil$Retention.Time, pch=as.integer(msqc1_dil.norm$Peptide.Sequence), col=msqc1_dil.norm$instrument, xlim=c(0,100)) legend("bottomright", as.character(unique(msqc1_dil.norm$instrument)), col= unique(msqc1_dil.norm$instrument), pch=as.integer(unique(msqc1_dil.norm$instrument))) ## ---- cache=FALSE-------------------------------------------------------- sessionInfo()