Intensity extraction and normalization algorithm development for DNA microarray image processing
Microarray has several thousands of spots that represent various parts of human genes on a slide. Each of the spot consists of two samples (normal as a reference and cancer as a target). The samples are labeled into green (reference) and red (target) dyes. If the spot is indicating green dye, it...
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my-unimap-774172022-12-07T00:59:29Z Intensity extraction and normalization algorithm development for DNA microarray image processing Asral, Bahari Jambek, Assoc. Prof. Dr. Microarray has several thousands of spots that represent various parts of human genes on a slide. Each of the spot consists of two samples (normal as a reference and cancer as a target). The samples are labeled into green (reference) and red (target) dyes. If the spot is indicating green dye, it shows a high expression of the normal sample whereas red dye shows a high expression of the target spotted on that gene. In order to indicate the percentage of red and green intensity for every spot, microarray undergoes image processing where there are huge amount of data that increase the probability of error and consume much time. Applying the image processing clears unwanted residues on the microarray image and solves the spot finding problem with high accuracy and short time consumption. The image processing involves gridding, segmentation, intensity extraction and normalization. Gridding addresses the spots on the microarray image. Then segmentation can perform separation between the foreground and background pixels. Thirdly, the averages of the foreground and background intensity for each spot are computed. Fourthly, unwanted balance of the colors is balanced to cut back the noises. The aim of this work is to improve the intensity extraction and normalization step for DNA microarray image processing algorithm using MATLAB. Three methods for allocating and calculating the background intensity values were discussed and compared. These methods were GenePix, ScanAlyze, and QuantArry. Besides that, five alternatives for intensity extraction were applied to a microarray slide image in order to find the most accurate intensity value for each spot in the two-color microarray. These alternatives were Standard, Kooperberg, Edward, Morph and No-background. Based on the results, Edward method shows the most accurate results to extract foreground and background intensity and to calculate the ultimate intensity for each spot by 39.7 dB in term of PSNR. An improved method was proposed for intensity extraction by increasing background locations, where this method showed very accurate results by 41.36 dB in term of PSNR and 2.2 in term of RMSE. Besides that, using the proposed method the MAE is around 9 while it is very high for the other intensity extraction existing algorithms. On the other hand, five normalization algorithms, Global, Lowess, Housekeeping, Quantile, and Print-tip, have been tested and compared to find the most suitable approach for normalization process. Print Tip normalization was chosen for normalization because of its high accuracy which was around 32.89 dB in term of PSNR and its final MA graph shape was well normalized. In relation to this matter, a proposed method for normalization was applied. It increases the accuracy by 33.15 dB in term of PSNR, 32.63 in term of MSE and the occurrence of errors become very small by around 12 in term of MAE. Finally, algorithm profiling has been done, it proved that the proposed algorithm consumes less time than the Bemis project by around 347.7 milliseconds. Universiti Malaysia Perlis (UniMAP) Thesis en http://dspace.unimap.edu.my:80/xmlui/handle/123456789/77417 http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/4/license.txt 8a4605be74aa9ea9d79846c1fba20a33 http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/1/Page%201-24.pdf 92e96b6e8bb4ac9774fd737678d29d91 http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/2/Full%20text.pdf e523f0aecc15d95a6eadf2394f2f9796 http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/3/Declaration%20Form.pdf 37c0ef603f2786310e12835ae90a749c Universiti Malaysia Perlis (UniMAP) DNA microarrays Image processing Image processing -- Digital techniques School of Microelectronic Engineering |
| institution |
Universiti Malaysia Perlis |
| collection |
UniMAP Institutional Repository |
| language |
English |
| advisor |
Asral, Bahari Jambek, Assoc. Prof. Dr. |
| topic |
DNA microarrays Image processing Image processing -- Digital techniques |
| spellingShingle |
DNA microarrays Image processing Image processing -- Digital techniques Intensity extraction and normalization algorithm development for DNA microarray image processing |
| description |
Microarray has several thousands of spots that represent various parts of human genes
on a slide. Each of the spot consists of two samples (normal as a reference and cancer as
a target). The samples are labeled into green (reference) and red (target) dyes. If the spot
is indicating green dye, it shows a high expression of the normal sample whereas red
dye shows a high expression of the target spotted on that gene. In order to indicate the
percentage of red and green intensity for every spot, microarray undergoes image
processing where there are huge amount of data that increase the probability of error
and consume much time. Applying the image processing clears unwanted residues on
the microarray image and solves the spot finding problem with high accuracy and short
time consumption. The image processing involves gridding, segmentation, intensity
extraction and normalization. Gridding addresses the spots on the microarray image.
Then segmentation can perform separation between the foreground and background
pixels. Thirdly, the averages of the foreground and background intensity for each spot
are computed. Fourthly, unwanted balance of the colors is balanced to cut back the
noises. The aim of this work is to improve the intensity extraction and normalization
step for DNA microarray image processing algorithm using MATLAB. Three methods
for allocating and calculating the background intensity values were discussed and
compared. These methods were GenePix, ScanAlyze, and QuantArry. Besides that, five
alternatives for intensity extraction were applied to a microarray slide image in order to
find the most accurate intensity value for each spot in the two-color microarray. These
alternatives were Standard, Kooperberg, Edward, Morph and No-background. Based on
the results, Edward method shows the most accurate results to extract foreground and
background intensity and to calculate the ultimate intensity for each spot by 39.7 dB in
term of PSNR. An improved method was proposed for intensity extraction by increasing
background locations, where this method showed very accurate results by 41.36 dB in
term of PSNR and 2.2 in term of RMSE. Besides that, using the proposed method the
MAE is around 9 while it is very high for the other intensity extraction existing
algorithms. On the other hand, five normalization algorithms, Global, Lowess, Housekeeping,
Quantile, and Print-tip, have been tested and compared to find the most
suitable approach for normalization process. Print Tip normalization was chosen for
normalization because of its high accuracy which was around 32.89 dB in term of
PSNR and its final MA graph shape was well normalized. In relation to this matter, a
proposed method for normalization was applied. It increases the accuracy by 33.15 dB
in term of PSNR, 32.63 in term of MSE and the occurrence of errors become very small
by around 12 in term of MAE. Finally, algorithm profiling has been done, it proved that
the proposed algorithm consumes less time than the Bemis project by around 347.7
milliseconds. |
| format |
Thesis |
| title |
Intensity extraction and normalization algorithm development for DNA microarray image processing |
| title_short |
Intensity extraction and normalization algorithm development for DNA microarray image processing |
| title_full |
Intensity extraction and normalization algorithm development for DNA microarray image processing |
| title_fullStr |
Intensity extraction and normalization algorithm development for DNA microarray image processing |
| title_full_unstemmed |
Intensity extraction and normalization algorithm development for DNA microarray image processing |
| title_sort |
intensity extraction and normalization algorithm development for dna microarray image processing |
| granting_institution |
Universiti Malaysia Perlis (UniMAP) |
| granting_department |
School of Microelectronic Engineering |
| url |
http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/1/Page%201-24.pdf http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/2/Full%20text.pdf http://dspace.unimap.edu.my:80/xmlui/bitstream/123456789/77417/3/Declaration%20Form.pdf |
| _version_ |
1776104276073906176 |