Description Usage Arguments Details Value Examples

Does a first-pass analysis for a comparative experiment. This includes the calculation of means and confidence intervals for the groups, and finally a Kruskal-Wallis p-value for the null hypothesis of no difference

1 |

`data` |
A data frame with one array in each column |

`probes` |
a vector containing the names of the probes in the same order as rows in D |

`g` |
A vector with the groups for the arrays, eg. TREATMENT and CONTROL |

`present` |
A dataframe with the Present calls, 3 = P, 2 = M, 1 = A. |

`log` |
if TRUE then data are log transformed through t(x) = log(1+x) and geometric means are calculated |

`labels` |
a vector of labels given the group means |

`output.data` |
if T the raw data are included in the output |

A speed-up for Wilcoxon based on Kronecker products was put in place with SAGx v.1.4.5. Ties are currently not taken into account in Wilcoxon.

A dataframe with the coumns PROBES, followed by group means and sd's, lower confidence intervals and then, upper confidence interval (confidence level 95%), and followed a Kruskal-Wallis p-value, and finally the input data,. If present names a dataframe holding the present calls the proportion present is calculated. Furthermore, if there are two groups the difference in group means is added.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## Not run:
# not run
g <- c(rep(1,4),rep(2,4)); labs <- c("Mean Diet","Mean Control"); probes <- paste("Probe",1:1000)
firstpass(data = utmat[1:2,], probes = probes[1:2], g, log = FALSE, labels = labs)
# Probesets Mean Diet Mean Control LCL.1 LCL.2 UCL.1 UCL.2 pval
#1 Probe 1 -12.3444460036497 -11.7495704973055 -12.9047961446666 -12.2832657957485 -11.7840958626327 -11.2158751988625 0.0433081428107922
#2 Probe 2 -7.99773926405627 -8.02799133391929 -8.47704512876227 -8.19487551919835 -7.51843339935028 -7.86110714864023 0.772829992684449
# Difference Subject 1 Subject 2 Subject 3 Subject 4 Subject 5 Subject 6 Subject 7 Subject 8
#1 -0.594875506344176 -12.345150 -11.805071 -12.776232 -12.451332 -11.595748 -12.320430 -11.482349 -11.599755
#2 0.0302520698630131 -7.660097 -8.157944 -8.404433 -7.768484 -7.979951 -8.017327 -8.197361 -7.917326
## End(Not run)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.