Question

我的数据设计矩阵如下所示。我运行命令来分析和比较不同的组，但得到错误。

我想进行这些比较： L4vsL6.L8， Q3vsQ5.Q7，QvsL

设计矩阵：

design

                organoids_biological_samples   method
L4_D49_rep_1                              L4      L
L4_D49_rep_2                              L4      L
L6_L8_D49_rep_1                        L6_L8      L
L6_L8_D49_rep_2                        L6_L8      L
Q3_D49_rep_1                              Q3      Q
Q3_D49_rep_2                              Q3      Q
Q5_Q7_D49_rep_1                        Q5_Q7      Q
Q5_Q7_D49_rep_2                        Q5_Q7      Q

design$organoids_biological_samples <- factor(design$organoids_biological_samples, levels = c("L4","L6_L8", "Q3", "Q5_Q7"))

design$method <- factor(design$method, levels = c("L", "Q"))

all(rownames(design) %in% colnames(data))

all(rownames(design) == colnames(data))

Group <- factor(paste(design$organoids_biological_samples,design$method,sep="."))

design<- cbind(design,Group)

design.matrix <- model.matrix(~0+Group+method,design)

colnames(design.matrix) <- c("L4.L", "L6_L8.L", "Q3.Q", "Q5_Q7.Q", "method")

design.matrix

                L4.L  L6_L8.L  Q3.Q  Q5_Q7.Q  method
L4_D49_rep_1       1       0    0       0      0
L4_D49_rep_2       1       0    0       0      0
L6_L8_D49_rep_1    0       1    0       0      0
L6_L8_D49_rep_2    0       1    0       0      0
Q3_D49_rep_1       0       0    1       0      1
Q3_D49_rep_2       0       0    1       0      1
Q5_Q7_D49_rep_1    0       0    0       1      1
Q5_Q7_D49_rep_2    0       0    0       1      1
attr(,"assign")
[1] 1 1 1 1 2
attr(,"contrasts")
attr(,"contrasts")$Group
[1] "contr.treatment"

attr(,"contrasts")$method
[1] "contr.treatment"

edgeR.dgelist = DGEList(counts = data,group = Group)

edgeR.dgelist = calcNormFactors(edgeR.dgelist,method = "TMM")

CommonDisp <- estimateGLMCommonDisp(edgeR.dgelist, design.matrix)

Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset,  : 
  Design matrix not of full rank.  The following coefficients not estimable:
 method

Answer 1

您的数据中存在严格的线性依赖： Q3.Q + Q5_Q7.Q = method。因此，您的模型无法为这些列找到唯一系数如果B1, B2, B3是最佳系数集，那么对于任何实数B1-x, B2-x, B3-x，x都是Text Qualifier。

在数值上，您的程序无法反转矩阵以找到最佳系数。考虑测试是否更好地在模型中包含Q3.Q和Q5_Q7.Q或仅包含方法。

设计矩阵中的错误：＆＃34;设计矩阵不是满秩。以下系数不可估计＆＃34;

1 个答案: