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Sample GSM2136

Query DataSets for GSM2136

Status

Public on Jun 27, 2002

Title

K562A-repro

Sample type

RNA

Channel 1

Source name

Reference Pool

Organism

Extracted molecule

total RNA

Channel 2

Source name

K562A

Organism

Extracted molecule

total RNA

Description

Category: Cell-line
Subcategory: Reproducibility
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = dtp3306

Submission date

Jun 21, 2002

Last update date

Nov 21, 2005

Organization

Stanford Microarray Database (SMD)

E-mail(s)

array@genome.stanford.edu

Phone

650-498-6012

URL

http://genome-www5.stanford.edu/

Department

Stanford University, School of Medicine

Street address

300 Pasteur Drive

City

Stanford

State/province

CA

ZIP/Postal code

94305

Country

USA

Platform ID

Series (1)

Human cancer cell lines

Data table header descriptions
ID_REF
CH1B_MEAN	mean channel 1 background
CH1B_MEDIAN	median channel 1 background
CH1D_MEAN	difference between CH1I_MEAN and CH1B_MEAN
CH2I_MEAN	mean channel 2 signal
CH2D_MEAN	difference of CH2I_MEAN and CH2B_MEAN
CH2B_MEAN	mean of channel 2 background
CH2B_MEDIAN	median of channel 2 background
CH2BN_MEDIAN	normalized CH2B_MEDIAN
CH2DN_MEAN	normalized CH2D_MEAN
CH2IN_MEAN	normalized CH2I_MEAN
CORR	simple correlation coefficient of channel 1 and channel 2 pixels
FLAG	user defined flag (default=0)
VALUE	same as UNF_VALUE but with flagged values removed
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD	standard deviation of fraction of pixels greater than CH1B_MEAN
PERGTBCH2I_1SD	standard deviation of fraction of pixels greater than CH2B_MEAN
RAT1_MEAN	ratio of CH1D_MEAN to CH2D_MEAN
RAT1N_MEAN	ratio of CH1DN_MEAN to CH2DN_MEAN
RAT2_MEAN	ratio of CH2D_MEAN to CH1D_MEAN
RAT2N_MEAN	ratio of CH2DN_MEAN and CH1DN_MEAN
REGR	slope of the simple regression line of channel 2 to channel 1 pixels
TOT_BPIX	total number of background pixels
TOT_SPIX	total number of signal (spot) pixels
TOP	vertical, short-axis spot ellipse minimum pixel coordinate
BOT	vertical, short-axis spot ellipse maximum pixel coordinate
LEFT	horizontal, long-axis spot ellipse minimum pixel coordinate
RIGHT	horizontal, long-axis spot ellipse maximum pixel coordinate
UNF_VALUE	aka LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN

Data table
ID_REF	CH1B_MEAN	CH1B_MEDIAN	CH1D_MEAN	CH2I_MEAN	CH2D_MEAN	CH2B_MEAN	CH2B_MEDIAN	CH2BN_MEDIAN	CH2DN_MEAN	CH2IN_MEAN	CORR	FLAG	VALUE	PIX_RAT2_MEDIAN	PERGTBCH1I_1SD	PERGTBCH2I_1SD	RAT1_MEAN	RAT1N_MEAN	RAT2_MEAN	RAT2N_MEAN	REGR	TOT_BPIX	TOT_SPIX	TOP	BOT	LEFT	RIGHT	UNF_VALUE
1	2216	2200		856		891	880	946		920	.533	0		1	0	0			0		.299	1131	52	14	22	42	50
2	2193	2176		840		901	880	946		903	.538	0		.5	0	0			0		.411	962	52	13	21	50	58
3	2142	2128	18	856		899	880	946		920	.33	0		.556	0	0					.239	810	52	13	21	59	67
4	2108	2096		862		896	880	946		926	.295	0		.138	0	0			0		.207	828	52	13	21	68	76
5	2077	2056	69	892	12	903	880	946	13	959	.335	0	-2.408	.417	0	0	5.75	5.308	.174	.188	.286	822	52	13	21	76	84	-2.408
6	2040	2024		853		905	888	954		917	.317	0		1.059	0	0			0		.307	822	52	13	21	85	93
7	2007	2000		890	2	901	888	954	2	956	.159	0		.522	0	0			0		.129	828	52	13	21	94	102
8	1996	1976		878		909	896	963		944	.106	0		.688	0	0			0		.081	828	52	13	21	103	111
9	1996	1968		896		922	904	972		963	.265	0		.36	0	1			0		.226	822	52	13	21	111	119
10	1983	1960	133	1025	113	931	912	980	122	1102	.439	0	-.125	1.056	0	13	1.177	1.09	.85	.917	.315	822	52	13	21	120	128	-.125
11	1974	1952	131	918	6	932	912	980	7	987		0	-4.226	.171	0	0	21.833	18.714	.046	.053		828	52	13	21	129	137	-4.226
12	1977	1960	57	990	70	936	920	989	75	1064	.303	0	.396	.862	1	5	.814	.76	1.228	1.316	.247	828	52	13	21	138	146	.396
13	1945	1952		862		934	920	989		926	.172	0		1	0	0			0		.119	822	52	13	21	146	154
14	1929	1936		898		930	920	989		965	.158	0		.692	0	1			0		.126	822	52	13	21	155	163
15	1926	1928	30	899		936	928	997		966	.047	0		.318	0	0					.025	828	52	13	21	164	172
16	1929	1936	3	910		946	944	1015		978	.151	0		.365	0	0					.076	828	52	13	21	173	181
17	1924	1920		924		953	944	1015		993	.118	0		.222	0	0			0		.061	822	52	13	21	181	189
18	1917	1904		939		975	952	1023		1009	.267	0		.409	0	0			0		.32	810	52	13	21	190	198
19	1898	1888	111	854		987	968	1040		918	.251	0		.421	0	0					.334	828	52	13	21	199	207
20	1888	1872		914		1002	984	1058		982	.322	0		12.22	0	1			0		.578	822	52	13	21	207	215

Total number of rows: 9984

Table truncated, full table size 1247 Kbytes.

Supplementary data files not provided

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