GSE7603: Human TALL tumor vs Normal Human DNA (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE7603)
GSM183878~ GSM183885
Except GSM183881, other samples all have dye-swap replicates.
Platform: Agilent-014693 Human Genome CGH Microarray 244A (G4411B)
Cy3 Channel: TALL tumor / Normal Human DNA
Cy5 Channel: Normal Human DNA / TALL tumor

GSM183879 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183879 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183880 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183880 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183881 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183882 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183882 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183883 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183883 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183884 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183884 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183885 – 1 Cy3 TALL tumor, Cy5 Normal Human DNA

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.

GSM183885 – 2 Cy3 Normal Human DNA, Cy5 TALL tumor

(I)   (II)   (III)

(I) 2D density distribution plot. X-axis is the log2 intensity of sample channel, Y-axis is the log2 intensity of reference channel.
(II) The illustration of the simulated data. (a) is the histogram of raw data ratio. (b) is the histogram of normalized ratio using spline curve fitting as the regression method (without moving-median filter). (c) is the histogram of normalized ratio with moving-median filter. (d) is the density plot by using EM algorithm.
(III) The results of aCGH ratio after implementing aCGH normalization.