adv2_microarray.ipynb

Kernel: Python 3

from __future__ import division, print_function
%matplotlib inline

DNA microarray processing

Data in this example

Yeast microarrays for genome wide parallel genetic and gene expression analysis

Two-color fluorescent scan of a yeast microarray containing 2,479 elements (ORFs). The center-to-center distance between elements is 345 μm. A probe mixture consisting of cDNA from yeast extract/peptone (YEP) galactose (green pseudocolor) and YEP glucose (red pseudocolor) grown yeast cultures was hybridized to the array. Intensity per element corresponds to ORF expression, and pseudocolor per element corresponds to relative ORF expression between the two cultures.

by Deval A. Lashkari, http://www.pnas.org/content/94/24/13057/F1.expansion

Learn more about microarrays:

• Tutorial on how to analyze microarray data

• Complementary DNA

More example data:

• MicroArray Genome Imaging & Clustering Tool by Laurie Heyer & team, Davidson College

import matplotlib.pyplot as plt

import numpy as np

from skimage import io, img_as_float

microarray = io.imread('../images/microarray.jpg')

# Scale between zero and one
microarray = img_as_float(microarray)

plt.figure(figsize=(10, 5))
plt.imshow(microarray[:500, :1000], cmap='gray', interpolation='nearest');

from skimage import color
f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))

red = microarray[..., 0]
green = microarray[..., 1]

red_rgb = np.zeros_like(microarray)
red_rgb[..., 0] = red

green_rgb = np.zeros_like(microarray)
green_rgb[..., 1] = green

ax0.imshow(green_rgb, interpolation='nearest')
ax1.imshow(red_rgb, interpolation='nearest')
plt.suptitle('\n\nPseudocolor plots of red and green channels', fontsize=16);

from skimage import filter as filters

mask = (green > 0.1)
plt.imshow(mask[:1000, :1000], cmap='gray');

z = red.copy()
z /= green
z[~mask] = 0

print(z.min(), z.max())

plt.imshow(z[:500, :500], cmap=plt.cm.gray, vmin=0, vmax=2);

Locating the grid

both = (green + red)

plt.imshow(both, cmap='gray');

from skimage import feature

sum_down_columns = both.sum(axis=0)
sum_across_rows = both.sum(axis=1)

dips_columns = feature.peak_local_max(sum_down_columns.max() - sum_down_columns)
dips_columns = dips_columns.ravel()

M = len(dips_columns)
column_distance = np.mean(np.diff(dips_columns))

dips_rows = feature.peak_local_max(sum_across_rows.max() - sum_across_rows)
dips_rows = dips_rows.ravel()

N = len(dips_rows)
row_distance = np.mean(np.diff(dips_rows))

print('Columns are a mean distance of %.2f apart' % column_distance)
print('Rows are a mean distance of %.2f apart' % row_distance)

f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 5))

ax0.plot(sum_down_columns)
ax0.scatter(dips_columns, sum_down_columns[dips_columns])
ax0.set_xlim(0, 200)
ax0.set_title('Column gaps')

ax1.plot(sum_across_rows)
ax1.scatter(dips_rows, sum_across_rows[dips_rows])
ax1.set_xlim(0, 200)
ax0.set_title('Row gaps');

P, Q = 500, 500

plt.figure(figsize=(15, 10))
plt.imshow(microarray[:P, :Q])

for i in dips_rows[dips_rows < P]:
    plt.plot([0, Q], [i, i], 'm')

for j in dips_columns[dips_columns < Q]:
    plt.plot([j, j], [0, P], 'm')

plt.axis('image');

out = np.zeros(microarray.shape[:2])

for i in range(M - 1):
    for j in range(N - 1):
        row0, row1 = dips_rows[i], dips_rows[i + 1]
        col0, col1 = dips_columns[j], dips_columns[j + 1]
        
        r = microarray[row0:row1, col0:col1, 0]
        g = microarray[row0:row1, col0:col1, 1]
        
        ratio = r / g
        mask = ~np.isinf(ratio)

        mean_ratio = np.mean(ratio[mask])
        if np.isnan(mean_ratio):
            mean_ratio = 0
        
        out[row0:row1, col0:col1] = mean_ratio

f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))

ax0.imshow(microarray)
ax0.grid(color='magenta', linewidth=1)

ax1.imshow(out, cmap='gray', interpolation='nearest', vmin=0, vmax=3);
ax1.grid(color='magenta', linewidth=1)

Transform the intensity to spot outliers

f, (ax0, ax1) = plt.subplots(1, 2, figsize=(15, 10))

ax0.imshow(microarray)
ax0.grid(color='magenta', linewidth=1)

ax1.imshow(np.log(0.5 + out), cmap='gray', interpolation='nearest', vmin=0, vmax=3);
ax1.grid(color='magenta', linewidth=1)

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%reload_ext load_style
%load_style ../themes/tutorial.css