limma包主要生成和使用6種數(shù)據(jù)對(duì)象(data objects)
EListRaw
全稱Raw Expression list. 儲(chǔ)存normalization前的single-channel raw intensities. Intensities沒(méi)有進(jìn)行l(wèi)og轉(zhuǎn)換欣尼。1個(gè)探針1行楣黍,1個(gè)array1列。
例:函數(shù)read.ilmn() 可以生成EListRaw
EList
全稱Expression list. 進(jìn)行過(guò)背景校正(background correct)和歸一化的log-intensities.
例:EListRaw輸入至normalizeBetweenArrays() 或neqc()會(huì)輸出EList肤无。
RGList
全稱Red-Green list. A class used to store raw two-color intensities as they are read in from an image analysis output file,
例:read.maimages()函數(shù)輸出RGList
MAList
全稱Two-color intensities converted to M-values and A-values,“ i.e., to within-spot and wholespot contrasts on the log-scale. ”(這句不太明白氢妈,spot怎么理解)
例:RGList輸入至MA.RG() 或normalizeWithinArrays()函數(shù)輸出MAList婿崭。
該對(duì)象每1個(gè)spot 1行怠惶,可能有多個(gè)spot因此每1個(gè)探針有多個(gè)行對(duì)應(yīng)
MArrayLM
全稱MicroArray Linear Model.
Store the result of fitting gene-wise linear models to the normalized intensities or log-ratios(log-ratios是怎么得到的).
例:由lmFit()函數(shù)輸出. 每1個(gè)探針1行
TestResults
Store the results of testing a set of contrasts equal to zero for each probe. (contrast怎么理解)
例:由decideTests()函數(shù)輸出. 每1個(gè)探針1行
操作以上六種數(shù)據(jù)對(duì)象同操作R中的list對(duì)象一樣
例:MAListcoef可以提取該對(duì)象的系數(shù)。也可以通過(guò)操作矩陣的方式操縱上述對(duì)象正林。如summary, dim, length, ncol, nrow, dimnames, rownames, colnames泡一。也可以用cbind, rbind, merge合并多個(gè)數(shù)據(jù)對(duì)象,例如cbind(RG1, RG2)觅廓。