Description Usage Arguments Details Value Author(s) Examples

These functions summarize columns of a matrix when the rows of the matrix are classified into different groups

1 2 3 4 5 6 7 8 9 10 11 | ```
subColSummarizeAvg(y, group.labels)
subColSummarizeAvgLog(y, group.labels)
subColSummarizeBiweight(y, group.labels)
subColSummarizeBiweightLog(y, group.labels)
subColSummarizeLogAvg(y, group.labels)
subColSummarizeLogMedian(y, group.labels)
subColSummarizeMedian(y, group.labels)
subColSummarizeMedianLog(y, group.labels)
subColSummarizeMedianpolish(y, group.labels)
subColSummarizeMedianpolishLog(y, group.labels)
convert.group.labels(group.labels)
``` |

`y` |
A numeric |

`group.labels` |
A vector to be treated as a factor variable. This is used to assign each row to a group. NA values should be used to exclude rows from consideration |

These functions are designed to summarize the columns of a matrix where the rows of the matrix are assigned to groups. The summarization is by column across all rows in each group.

subColSummarizeAvgSummarize by taking mean

subColSummarizeAvgLog

`log2`

transform the data and then take means in column-wise mannersubColSummarizeBiweightUse a one-step Tukey Biweight to summarize columns

subColSummarizeBiweightLog

`log2`

transform the data and then use a one-step Tukey Biweight to summarize columnssubColSummarizeLogAvgSummarize by taking mean and then taking

`log2`

subColSummarizeLogMedianSummarize by taking median and then taking

`log2`

subColSummarizeMedianSummarize by taking median

subColSummarizeMedianLog

`log2`

transform the data and then summarize by taking mediansubColSummarizeMedianpolishUse the median polish to summarize each column, by also using a row effect (not returned)

subColSummarizeMedianpolishLog

`log2`

transform the data and then use the median polish to summarize each column, by also using a row effect (not returned)

A `matrix`

containing column summarized data. Each row
corresponds to data column summarized over a group of rows.

B. M. Bolstad <[email protected]>

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
### Assign the first 10 rows to one group and
### the second 10 rows to the second group
###
y <- matrix(c(10+rnorm(50),20+rnorm(50)),20,5,byrow=TRUE)
subColSummarizeAvgLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogAvg(y,c(rep(1,10),rep(2,10)))
subColSummarizeAvg(y,c(rep(1,10),rep(2,10)))
subColSummarizeBiweight(y,c(rep(1,10),rep(2,10)))
subColSummarizeBiweightLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedianLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeLogMedian(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedian(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedianpolishLog(y,c(rep(1,10),rep(2,10)))
subColSummarizeMedianpolish(y,c(rep(1,10),rep(2,10)))
``` |

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