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Spencer Goodman week05 homework: slightly late, but accurate to the 12th decimal pt #126

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Spencer Goodman week05 homework: slightly late, but accurate to the 12th decimal pt #126

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135 changes: 127 additions & 8 deletions weeks/week03/homework.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
"cell_type": "raw",
"metadata": {},
"source": [
" "
" this is a one tailed test because we expect the difference to be in a specific direction (in this case higher level in A then B alleles)"
]
},
{
Expand All @@ -36,7 +36,9 @@
{
"cell_type": "raw",
"metadata": {},
"source": []
"source": [
"in this case because the data appears to be non-parametric a test such as the wilcoxon sum ranked test would be most appropriate"
]
},
{
"cell_type": "markdown",
Expand All @@ -46,9 +48,60 @@
]
},
{
"cell_type": "raw",
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"\n",
"\tShapiro-Wilk normality test\n",
"\n",
"data: data_b$normal - data_c$normal\n",
"W = 0.97567, p-value = 0.9281\n"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"text/plain": [
"\n",
"\tWilcoxon rank sum test\n",
"\n",
"data: data_b$normal and data_c$normal\n",
"W = 6, p-value = 0.06494\n",
"alternative hypothesis: true location shift is not equal to 0\n"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data <- read.table(file = \"adamts_B6.txt\", header = TRUE)\n",
"\n",
"data_b <- subset(data, subset = nxf1 == \"B\")\n",
"data_c <- subset(data, subset = nxf1 == \"C\")\n",
"\n",
"shapiro.test(data_b$normal-data_c$normal)\n",
"\n",
"wilcox.test(x = data_b$normal, y = data_c$normal)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
"source": [
"Since the p value is larger then 0.05, we conclude that there is no sigificant difference between the alleles. "
]
},
{
"cell_type": "markdown",
Expand All @@ -60,9 +113,71 @@
]
},
{
"cell_type": "raw",
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Warning message:\n",
"In data_b$normal.f2 - data_c$normal.f2: longer object length is not a multiple of shorter object length"
]
},
{
"data": {
"text/plain": [
"\n",
"\tShapiro-Wilk normality test\n",
"\n",
"data: data_b$normal.f2 - data_c$normal.f2\n",
"W = 0.81146, p-value = 0.002215\n"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"text/plain": [
"\n",
"\tWelch Two Sample t-test\n",
"\n",
"data: data_b$normal.f2 and data_c$normal.f2\n",
"t = -2.0766, df = 13.225, p-value = 0.02894\n",
"alternative hypothesis: true difference in means is less than 0\n",
"95 percent confidence interval:\n",
" -Inf -0.0005380758\n",
"sample estimates:\n",
" mean of x mean of y \n",
"0.002613228 0.006241535 \n"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data <- read.table(file = \"adamts_balbF2.txt\", header = TRUE)\n",
"\n",
"data_b <- subset(data, subset = nxf1.f2 == \"B\")\n",
"data_c <- subset(data, subset = nxf1.f2 == \"C\")\n",
"\n",
"shapiro.test(data_b$normal.f2-data_c$normal.f2)\n",
"t.test(data_b$normal.f2, data_c$normal.f2, alternative = \"less\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
"source": [
"I conclude that since the data is normally distributed, a t-test is appropriate in this case. Furthermore, since we expect the B allele to be higher, a one-tailed test is also approriate. Given these conditions, I reject the null hypothesis and conclude that the B allele is significantly higher than C."
]
},
{
"cell_type": "markdown",
Expand All @@ -74,7 +189,9 @@
{
"cell_type": "raw",
"metadata": {},
"source": []
"source": [
"I conclude that Nfx1 has an influcence on Gene 8 in a strain-specific fashion. The evidence is not overwhelming of an effect, then. However, the p value for B6 is very close to significant. Further experiments are validated."
]
},
{
"cell_type": "markdown",
Expand All @@ -86,7 +203,9 @@
{
"cell_type": "raw",
"metadata": {},
"source": []
"source": [
"Parametric tests are more senstitive. This is why non-parametric tests use ranks."
]
},
{
"cell_type": "markdown",
Expand Down