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week04 HW #120

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week04 HW #120

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78615ba
add work up to exercise 2
csauvey Jan 20, 2016
c87e72b
Merge remote-tracking branch 'upstream/master'
csauvey Jan 20, 2016
ed0e22b
adding hw2
csauvey Jan 20, 2016
a53cddb
merge
csauvey Jan 21, 2016
6288fd3
Merge branch 'master' of https://github.com/biom262/biom262-2016
csauvey Jan 26, 2016
eb61b11
uploading hw week04
csauvey Jan 29, 2016
7958bac
commiting mann_whitney and alignment_expression_quantification
csauvey Feb 16, 2016
0e26e44
alignment again
csauvey Feb 16, 2016
8c9400b
HW4 1st draft
csauvey Feb 17, 2016
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2 changes: 1 addition & 1 deletion weeks/week01/7_tf_binding_promoters.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1301,4 +1301,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
23 changes: 19 additions & 4 deletions weeks/week02/homework2.ipynb
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196 changes: 117 additions & 79 deletions weeks/week03/02_Mann_Whitney.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -549,21 +549,11 @@
},
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"The following objects are masked from ad13b (pos = 5):\n",
"\n",
" cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n",
"\n"
]
},
{
"data": {
"text/html": [
Expand Down Expand Up @@ -597,7 +587,7 @@
"[1] \"id.f2\" \"nxf1.f2\" \"raw.f2\" \"normal.f2\" \"cohort.f2\""
]
},
"execution_count": 41,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -617,22 +607,28 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in stopifnot(is.numeric(x)): object 'normal' not found\n",
"output_type": "error",
"traceback": [
"Error in stopifnot(is.numeric(x)): object 'normal' not found\n"
]
"data": {
"text/plain": [
"\n",
"\tShapiro-Wilk normality test\n",
"\n",
"data: normal.f2[1:6]\n",
"W = 0.63073, p-value = 0.001059\n"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"shapiro.test(normal[1:6])"
"shapiro.test(normal.f2[1:6])"
]
},
{
Expand All @@ -644,22 +640,28 @@
},
{
"cell_type": "code",
"execution_count": 43,
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in stopifnot(is.numeric(x)): object 'normal' not found\n",
"output_type": "error",
"traceback": [
"Error in stopifnot(is.numeric(x)): object 'normal' not found\n"
]
"data": {
"text/plain": [
"\n",
"\tShapiro-Wilk normality test\n",
"\n",
"data: normal.f2[7:12]\n",
"W = 0.92503, p-value = 0.5423\n"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"shapiro.test(normal[7:12])"
"shapiro.test(normal.f2[7:12])"
]
},
{
Expand All @@ -671,22 +673,29 @@
},
{
"cell_type": "code",
"execution_count": 44,
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in wilcox.test(normal[1:6], normal[7:12], paired = F, alternative = \"less\"): object 'normal' not found\n",
"output_type": "error",
"traceback": [
"Error in wilcox.test(normal[1:6], normal[7:12], paired = F, alternative = \"less\"): object 'normal' not found\n"
]
"data": {
"text/plain": [
"\n",
"\tWilcoxon rank sum test\n",
"\n",
"data: normal.f2[1:6] and normal.f2[7:12]\n",
"W = 14, p-value = 0.2944\n",
"alternative hypothesis: true location shift is less than 0\n"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"wilcox.test(normal[1:6],normal[7:12],paired=F,alternative=\"less\")"
"wilcox.test(normal.f2[1:6],normal.f2[7:12],paired=F,alternative=\"less\")"
]
},
{
Expand All @@ -698,31 +707,44 @@
},
{
"cell_type": "code",
"execution_count": 45,
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n",
"evalue": "Error in file(con, \"rb\"): cannot open the connection\n",
"output_type": "error",
"traceback": [
"Error in eval(expr, envir, enclos): object 'normal' not found\n"
"Error in file(con, \"rb\"): cannot open the connection\n"
]
},
{
"ename": "ERROR",
"evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n",
"evalue": "Error in file(con, \"rb\"): cannot open the connection\n",
"output_type": "error",
"traceback": [
"Error in eval(expr, envir, enclos): object 'normal' not found\n"
"Error in file(con, \"rb\"): cannot open the connection\n"
]
},
{
"data": {
"text/plain": [
"plot without title"
]
},
"metadata": {
"image/svg+xml": {
"isolated": true
}
},
"output_type": "display_data"
}
],
"source": [
"plot(normal~nxf1)\n",
"points(normal~nxf1,col=\"darkgreen\")"
"plot(normal.f2~nxf1.f2)\n",
"points(normal.f2~nxf1.f2,col=\"darkgreen\")"
]
},
{
Expand All @@ -734,7 +756,7 @@
},
{
"cell_type": "code",
"execution_count": 46,
"execution_count": 8,
"metadata": {
"collapsed": false
},
Expand All @@ -743,11 +765,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"The following objects are masked from ad13b (pos = 3):\n",
"\n",
" cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n",
"\n",
"The following objects are masked from ad13b (pos = 6):\n",
"The following objects are masked from ad13b:\n",
"\n",
" cohort.f2, id.f2, normal.f2, nxf1.f2, raw.f2\n",
"\n"
Expand Down Expand Up @@ -786,7 +804,7 @@
"[1] \"id.f2\" \"nxf1.f2\" \"raw.f2\" \"normal.f2\" \"cohort.f2\""
]
},
"execution_count": 46,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -806,7 +824,7 @@
},
{
"cell_type": "code",
"execution_count": 47,
"execution_count": 9,
"metadata": {
"collapsed": false
},
Expand All @@ -821,7 +839,7 @@
"W = 0.70643, p-value = 9.494e-05\n"
]
},
"execution_count": 47,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -839,7 +857,7 @@
},
{
"cell_type": "code",
"execution_count": 48,
"execution_count": 10,
"metadata": {
"collapsed": false
},
Expand All @@ -854,7 +872,7 @@
"W = 0.62012, p-value = 0.0001587\n"
]
},
"execution_count": 48,
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -940,39 +958,38 @@
},
{
"cell_type": "code",
"execution_count": 51,
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n",
"output_type": "error",
"traceback": [
"Error in eval(expr, envir, enclos): object 'normal' not found\n"
]
},
{
"ename": "ERROR",
"evalue": "Error in eval(expr, envir, enclos): object 'normal' not found\n",
"output_type": "error",
"traceback": [
"Error in eval(expr, envir, enclos): object 'normal' not found\n"
"name": "stderr",
"output_type": "stream",
"text": [
"Warning message:\n",
"In wilcox.test.default(grpB, grpC, paired = F, alternative = \"less\"): cannot compute exact p-value with ties"
]
},
{
"ename": "ERROR",
"evalue": "Error in wilcox.test(grpB, grpC, paired = F, alternative = \"less\"): object 'grpB' not found\n",
"output_type": "error",
"traceback": [
"Error in wilcox.test(grpB, grpC, paired = F, alternative = \"less\"): object 'grpB' not found\n"
]
"data": {
"text/plain": [
"\n",
"\tWilcoxon rank sum test with continuity correction\n",
"\n",
"data: grpB and grpC\n",
"W = 124, p-value = 0.00999\n",
"alternative hypothesis: true location shift is less than 0\n"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"grpB<-c(normal.f2[1:18],normal[1:6])\n",
"grpC<-c(normal.f2[19:30],normal[7:12])\n",
"grpB<-c(normal.f2[1:18],normal.f2[1:6])\n",
"grpC<-c(normal.f2[19:30],normal.f2[7:12])\n",
"wilcox.test(grpB,grpC,paired=F,alternative=\"less\")"
]
},
Expand All @@ -985,18 +1002,39 @@
},
{
"cell_type": "code",
"execution_count": 52,
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in boxplot(grpB, grpC): object 'grpB' not found\n",
"evalue": "Error in file(con, \"rb\"): cannot open the connection\n",
"output_type": "error",
"traceback": [
"Error in file(con, \"rb\"): cannot open the connection\n"
]
},
{
"ename": "ERROR",
"evalue": "Error in file(con, \"rb\"): cannot open the connection\n",
"output_type": "error",
"traceback": [
"Error in boxplot(grpB, grpC): object 'grpB' not found\n"
"Error in file(con, \"rb\"): cannot open the connection\n"
]
},
{
"data": {
"text/plain": [
"plot without title"
]
},
"metadata": {
"image/svg+xml": {
"isolated": true
}
},
"output_type": "display_data"
}
],
"source": [
Expand Down
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