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Sample GSM72187

Query DataSets for GSM72187

Status

Public on Aug 27, 2005

Title

CLL-57

Sample type

RNA

Channel 1

Source name

Lymphopool

Organism

Characteristics

Lymphopool

Extracted molecule

total RNA

Label

Cy3

Channel 2

Source name

CLL-57

Organism

Characteristics

CLL-57

Extracted molecule

total RNA

Label

Cy5

Description

Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2646.gif

Data processing

VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

Submission date

Aug 26, 2005

Last update date

Sep 22, 2006

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)

Relation of Gene Expression Phenotype to Immunoglobulin Mutation Genotype in B Cell Chronic Lymphocytic Leukemia

Data table header descriptions
ID_REF	ID_REF
CH1I_MEAN	Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN	Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN	Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN	Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN	The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN	The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN	Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN	Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background
PERGTBCH1I_1SD	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PIX_RAT2_MEDIAN	Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX	Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX	Number of background pixels.; Type: integer; Scale: linear_scale
REGR	The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR	The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
TOP	Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT	Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT	Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT	Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG	User defined spot flag (default 0).; Type: integer; Scale: linear_scale
CH2IN_MEAN	Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN	Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN	Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN	Type: float; Scale: linear_scale
RAT1N_MEAN	Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
VALUE	same as UNF_VALUE but with flagged values removed
UNF_VALUE	Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF	CH1I_MEAN	CH2I_MEAN	CH1B_MEDIAN	CH2B_MEDIAN	CH1D_MEAN	CH2D_MEAN	CH1B_MEAN	CH2B_MEAN	PERGTBCH1I_1SD	PERGTBCH2I_1SD	PIX_RAT2_MEDIAN	TOT_SPIX	TOT_BPIX	REGR	CORR	TOP	BOT	LEFT	RIGHT	FLAG	CH2IN_MEAN	CH2BN_MEDIAN	CH2DN_MEAN	RAT2N_MEAN	RAT1N_MEAN	VALUE	UNF_VALUE
1	267	264	231	235	36	29	268	264	25	23	1.167	177	1142	.32	.363	86	101	32	47	0	713	635	78	2.167	.462	1.115	1.115
2	2395	2477	215	217	2180	2260	330	369	68	66	.98	177	918	1.013	.937	85	100	50	65	0	6694	586	6108	2.802	.357	1.486	1.486
3	3998	9138	209	215	3789	8923	362	365	75	81	2.269	177	893	0	0	85	100	67	82	0	24697	581	24116	6.365	.157	2.67	2.67
4	4909	971	212	224	4697	747	337	318	72	60	.157	177	928	0	0	84	99	84	99	0	2624	605	2019	.43	2.326	-1.218	-1.218
5	8995	8531	212	219	8783	8312	305	250	83	79	.852	177	919	0	0	84	99	102	117	0	23056	591	22465	2.558	.391	1.355	1.355
6	3101	2038	216	216	2885	1822	306	246	77	73	.623	177	906	.645	.921	84	99	119	134	0	5508	583	4925	1.707	.586	.772	.772
7	5845	2156	215	203	5630	1953	270	225	79	75	.324	177	919	0	0	83	98	137	152	0	5827	548	5279	.938	1.066	-.093	-.093
8	2884	1480	218	200	2666	1280	270	231	71	70	.46	177	906	.441	.877	83	98	154	169	0	4000	540	3460	1.298	.771	.376	.376
9	3649	1202	235	212	3414	990	291	241	75	72	.28	177	896	0	0	83	98	172	187	0	3248	572	2676	.784	1.276	-.351	-.351
10	2937	763	232	224	2705	539	290	250	72	64	.207	177	919	.188	.83	82	97	189	204	0	2062	605	1457	.539	1.857	-.893	-.893
11	6312	4437	225	231	6087	4206	299	256	79	80	.66	177	906	0	0	82	97	207	222	0	11991	624	11367	1.867	.535	.901	.901
12	7083	3178	224	232	6859	2946	301	263	81	78	.396	177	896	0	0	82	97	224	239	0	8589	627	7962	1.161	.861	.215	.215
13	338	285	210	224	128	61	256	245	38	24	.556	177	919	.308	.478	81	96	242	257	0	770	605	165	1.289	.776	.366	.366
14	3246	3432	207	227	3039	3205	286	354	77	77	1.066	177	906	0	0	81	96	259	274	0	9275	613	8662	2.85	.351	1.511	1.511
15	4422	9850	215	230	4207	9620	301	369	80	79	2.055	177	928	0	0	80	95	277	292	0	26621	621	26000	6.18	.162	2.628	2.628
16	7119	1320	216	227	6903	1093	264	306	81	72	.158	177	919	0	0	80	95	294	309	0	3567	613	2954	.428	2.337	-1.225	-1.225
17	11027	9561	209	220	10818	9341	236	233	84	88	.787	177	896	0	0	80	95	312	327	0	25840	594	25246	2.334	.429	1.223	1.223
18	4128	2578	210	218	3918	2360	246	234	79	81	.623	177	919	0	0	79	94	329	344	0	6967	589	6378	1.628	.614	.703	.703
19	7696	2400	207	228	7489	2172	245	240	83	78	.282	177	905	0	0	79	94	347	362	0	6486	616	5870	.784	1.276	-.351	-.351
20	4332	1776	207	223	4125	1553	240	235	86	83	.373	177	896	0	0	79	94	364	379	0	4800	602	4198	1.018	.983	.025	.025

Total number of rows: 18432

Table truncated, full table size 2173 Kbytes.

Supplementary data files not provided

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