181 lines
7.2 KiB
Plaintext
181 lines
7.2 KiB
Plaintext
## 问题：肠道微生物群落与多发性硬化症
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### 研究问题
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研究问题是：非致病性肠道微生物是否会触发实验性自身免疫性脑脊髓炎(EAE)的发作？
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研究问题是：[简明描述研究问题，形式为"A是否与B有关系？"或"A是否比B更[某种特性]？"]
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### 假设
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- 零假设(H0)：无菌(GF)小鼠和特定病原体清除(SPF)小鼠的自身反应性T细胞百分比没有显著差异。
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- 备择假设(H1)：特定病原体清除(SPF)小鼠的自身反应性T细胞百分比显著高于无菌(GF)小鼠。
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- 零假设(H0)：[组别A]和[组别B]的[测量变量]没有显著差异。
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- 备择假设(H1)：[组别A]的[测量变量]显著[高于/低于/不同于][组别B]。
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### 数据分析
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```{r}
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# 读取数据
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eae_data <- read.csv("c:/Users/31598/Desktop/BSI_exam/eae.csv", stringsAsFactors = TRUE)
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# 查看数据结构
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str(eae_data)
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head(eae_data)
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# 计算每组的描述性统计量
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tapply(eae_data$autoreactive, eae_data$group, summary)
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tapply(eae_data$autoreactive, eae_data$group, sd)
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# 箱线图
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boxplot(autoreactive ~ group, data = eae_data,
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main = "不同微生物环境下小鼠的自身反应性T细胞百分比",
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xlab = "小鼠组别",
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ylab = "自身反应性T细胞百分比 (%)",
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col = c("lightblue", "salmon"),
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border = "black")
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# 添加点以显示原始数据
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stripchart(autoreactive ~ group, data = eae_data,
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method = "jitter",
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vertical = TRUE,
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add = TRUE,
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pch = 19,
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col = "darkblue")
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# 小提琴图 (提供更多分布信息)
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if(!require(vioplot)) install.packages("vioplot")
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library(vioplot)
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with(eae_data,
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vioplot(autoreactive[group=="GF"],
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autoreactive[group=="SPF"],
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names = c("GF", "SPF"),
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col = c("lightblue", "salmon"),
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main = "不同微生物环境下小鼠的自身反应性T细胞百分比",
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xlab = "小鼠组别",
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ylab = "自身反应性T细胞百分比 (%)"))
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# 点图加均值和95%置信区间
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library(ggplot2)
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ggplot(eae_data, aes(x = group, y = autoreactive, color = group)) +
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geom_point(position = position_jitter(width = 0.2), size = 3, alpha = 0.7) +
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stat_summary(fun = mean, geom = "point", shape = 18, size = 5, color = "black") +
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stat_summary(fun.data = mean_cl_normal, geom = "errorbar", width = 0.2) +
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labs(title = "不同微生物环境下小鼠的自身反应性T细胞百分比",
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x = "小鼠组别",
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y = "自身反应性T细胞百分比 (%)") +
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theme_classic() +
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scale_color_manual(values = c("blue", "red"))
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```
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### 数据分析模板
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```{r}
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# 读取数据
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data <- read.csv("[数据文件路径]", stringsAsFactors = TRUE)
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# 查看数据结构
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str(data)
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head(data)
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# 计算每组的描述性统计量
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tapply(data$[测量变量], data$[分组变量], summary)
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tapply(data$[测量变量], data$[分组变量], sd)
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# 箱线图
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boxplot([测量变量] ~ [分组变量], data = data,
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main = "[图表标题]",
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xlab = "[x轴标签]",
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ylab = "[y轴标签]",
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col = c("lightblue", "salmon"),
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border = "black")
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# 添加点以显示原始数据
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stripchart([测量变量] ~ [分组变量], data = data,
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method = "jitter",
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vertical = TRUE,
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add = TRUE,
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pch = 19,
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col = "darkblue")
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# 可选：其他可视化方法
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# 小提琴图
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if(!require(vioplot)) install.packages("vioplot")
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library(vioplot)
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# 点图加均值和95%置信区间
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library(ggplot2)
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ggplot(data, aes(x = [分组变量], y = [测量变量], color = [分组变量])) +
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geom_point(position = position_jitter(width = 0.2), size = 3, alpha = 0.7) +
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stat_summary(fun = mean, geom = "point", shape = 18, size = 5, color = "black") +
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stat_summary(fun.data = mean_cl_normal, geom = "errorbar", width = 0.2) +
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labs(title = "[图表标题]",
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x = "[x轴标签]",
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y = "[y轴标签]") +
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theme_classic() +
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scale_color_manual(values = c("blue", "red"))
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```
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### 检验假设的统计检验
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```{r}
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# 由于我们有明确的方向性假设(SPF > GF)，使用单侧t检验
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t_test <- t.test(autoreactive ~ group, data = eae_data,
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alternative = "less", # GF < SPF
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var.equal = FALSE)
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t_test
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```
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### 检查统计检验的假设
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```{r}
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# 1. 检查正态性
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# 按组分别检查
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shapiro_GF <- shapiro.test(eae_data$autoreactive[eae_data$group == "GF"])
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shapiro_SPF <- shapiro.test(eae_data$autoreactive[eae_data$group == "SPF"])
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cat("GF组Shapiro-Wilk正态性检验 p值:", shapiro_GF$p.value, "\n")
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cat("SPF组Shapiro-Wilk正态性检验 p值:", shapiro_SPF$p.value, "\n")
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# Q-Q图
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par(mfrow = c(1, 2))
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qqnorm(eae_data$autoreactive[eae_data$group == "GF"], main = "GF组Q-Q图")
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qqline(eae_data$autoreactive[eae_data$group == "GF"])
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qqnorm(eae_data$autoreactive[eae_data$group == "SPF"], main = "SPF组Q-Q图")
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qqline(eae_data$autoreactive[eae_data$group == "SPF"])
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par(mfrow = c(1, 1))
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# 直方图
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par(mfrow = c(1, 2))
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hist(eae_data$autoreactive[eae_data$group == "GF"],
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main = "GF组直方图",
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xlab = "自身反应性T细胞百分比 (%)",
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col = "lightblue")
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hist(eae_data$autoreactive[eae_data$group == "SPF"],
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main = "SPF组直方图",
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xlab = "自身反应性T细胞百分比 (%)",
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col = "salmon")
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par(mfrow = c(1, 1))
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# 2. 检查方差同质性
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var_test <- var.test(autoreactive ~ group, data = eae_data)
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var_test
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# 3. 非参数检验 (如果正态性假设不满足)
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wilcox_test <- wilcox.test(autoreactive ~ group, data = eae_data,
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alternative = "less") # GF < SPF
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wilcox_test
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```
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### conclusion and discussion:
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研究问题是探究非致病性肠道微生物是否会触发实验性自身免疫性脑脊髓炎(EAE)的发作。我的分析流程如下：
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首先，我通过箱线图、小提琴图和点图等多种可视化方法展示了两组小鼠（GF和SPF）的自身反应性T细胞百分比数据。这些图表清晰地显示SPF组小鼠的自身反应性T细胞百分比明显高于GF组。
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在选择统计检验方法时，我考虑了数据的特性：
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1. 数据是两个独立组的连续测量值
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2. 我们有明确的方向性假设（SPF组高于GF组）
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3. 样本量相对较小（每组8只小鼠）
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基于这些特点，我首先选择了独立样本t检验（单侧）。为了验证t检验的假设，我进行了以下检查：
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1. 正态性检验：Shapiro-Wilk检验结果显示GF组p值为`r shapiro_GF$p.value`，SPF组p值为`r shapiro_SPF$p.value`，均大于0.05...
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2. 方差同质性检验：F检验结果p值为`r var_test$p.value`，大于0.05...
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3. t检验的p值为`r t_test$p.value`，显著小于0.05...
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4. Wilcoxon秩和检验，结果p值为`r wilcox_test$p.value`，同样支持拒绝零假设。
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结论是：特定病原体清除(SPF)小鼠的自身反应性T细胞百分比显著高于无菌(GF)小鼠。这表明非致病性肠道微生物确实会触发实验性自身免疫性脑脊髓炎(EAE)的发作。SPF小鼠体内存在非致病性肠道微生物，而这些微生物在GF小鼠中缺失，这种差异导致了SPF小鼠中更高比例的自身反应性T细胞，进而可能促进EAE的发展 |