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Sample GSM72172

Query DataSets for GSM72172

Status

Public on Aug 27, 2005

Title

CLL-25

Sample type

RNA

Channel 1

Source name

Lymphopool

Organism

Characteristics

Lymphopool

Extracted molecule

total RNA

Label

Cy3

Channel 2

Source name

CLL-25

Organism

Characteristics

CLL-25

Extracted molecule

total RNA

Label

Cy5

Description

Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2675.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	452	1001	465	976	null	25	489	1008	13	11	2.207	177	1142	.794	.41	67	82	92	107	-100	2539	2476	63	null	null		null
2	2466	1921	426	931	2040	990	454	953	48	42	.524	177	928	.411	.896	67	82	109	124	-100	4873	2362	2511	1.231	.812		.3
3	2720	5701	378	886	2342	4815	435	920	57	58	1.936	177	928	0	0	67	82	127	142	-100	14462	2247	12214	5.215	.192		2.383
4	3488	1391	340	844	3148	547	382	875	54	38	.204	177	928	0	0	67	82	144	159	-100	3529	2141	1388	.441	2.269		-1.182
5	4090	3321	345	810	3745	2511	469	927	68	61	.786	177	928	0	0	67	82	162	177	-100	8424	2055	6370	1.701	.588		.766
6	1950	1757	332	768	1618	989	611	1182	67	58	.664	177	928	.411	.688	67	82	179	194	-100	4457	1948	2509	1.551	.645		.633
7	5004	2411	286	745	4718	1666	495	1076	67	51	.523	177	950	0	0	67	82	197	212	-100	6116	1890	4226	.896	1.116		-.159
8	2732	1705	292	732	2440	973	311	758	64	52	.477	177	918	.281	.826	67	82	215	230	-100	4325	1857	2468	1.012	.989		.017
9	2856	1334	309	802	2547	532	326	837	58	38	.238	177	906	.177	.816	67	82	232	247	-100	3384	2034	1350	.53	1.887		-.916
10	2267	1497	331	924	1936	573	378	1138	53	42	.349	177	896	.244	.795	67	82	250	265	-100	3797	2344	1454	.751	1.332		-.414
11	6056	6304	335	1008	5721	5296	382	1234	72	55	.297	177	896	0	0	67	82	267	282	-100	15991	2557	13434	2.348	.426		1.232
12	4653	2777	333	1202	4320	1575	374	1291	61	48	.402	177	896	0	0	67	82	285	300	-100	7044	3049	3995	.925	1.081		-.113
13	546	2345	350	1636	196	709	558	1919	41	32	3.412	177	896	1.265	.518	67	82	302	317	-100	5948	4150	1798	9.176	.109		3.198
14	2405	3118	340	1618	2065	1500	528	1914	64	55	1.513	177	896	.356	.809	67	82	320	335	-100	7909	4104	3805	1.843	.543		.882
15	3849	8320	294	1102	3555	7218	331	1228	68	64	2.082	177	896	0	0	67	82	337	352	-100	21105	2795	18310	5.15	.194		2.365
16	4422	1732	264	846	4158	886	307	960	69	51	.241	177	919	0	0	67	82	355	370	-100	4394	2146	2247	.541	1.85		-.888
17	7473	5360	262	862	7211	4498	289	896	79	63	.591	177	896	0	0	67	82	373	388	-100	13597	2187	11410	1.582	.632		.662
18	2971	2526	263	903	2708	1623	287	933	69	56	.605	177	928	.54	.898	66	81	390	405	-100	6408	2291	4117	1.52	.658		.604
19	6847	3726	289	912	6558	2814	321	943	71	60	.483	177	928	0	0	66	81	408	423	-100	9452	2313	7138	1.088	.919		.122
20	3050	2188	289	869	2761	1319	328	904	61	55	.574	177	928	.344	.844	66	81	425	440	-100	5550	2204	3346	1.212	.825		.277

Total number of rows: 18432

Table truncated, full table size 2189 Kbytes.

Supplementary data files not provided

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