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Series GSE60486

Query DataSets for GSE60486

Status

Public on Sep 18, 2014

Title

Consensus Preprocessing of GEO and ArrayExpress Normal and Diseased Lung Tissue Microarray Data

Sample organism

Homo sapiens

Experiment type

Expression profiling by array
Third-party reanalysis

Summary

The Affymetrix oligonucleotide microarrays measure gene expression by quantifying intensity of fluorescently labeled gene fragments that bind to sets of 25-mer oligonucleotide probes on the chip with specific sequences tailored to be complementary to the target genes. Each gene is associated with a "probe set" containing several pairs (usually 11) of "perfect match" (perfectly complementary to target sequence) and "mismatch" (different base at position 13 of 25) probes. The raw measurements of each probe set consist of a set of intensities from the probes, which require in silico preprocessing by (1) correcting for background variability, (2) normalizing intensities across samples, and (3) summarizing intensities across the probe set into a single expression value. The output of the summarization step corresponds to the background-adjusted value for the mRNA of interest. We preprocess using GCRMA, which corrects for background variability by accounting for optical noise, probe affinity, and mismatch probe adjustment; normalizes intensities by quantile normalization; and summarizes intensities using a median polish method. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the dataset together. However, preprocessing across multple platforms requires a consolidation of probes with identical sequences, precluding global preprocessing on datasets with multiple platforms using the standard preprocessing pipelines. To address this problem, we have developed and applied a custom preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets.

Overall design

We preprocessed as a single dataset gene expression data collected from 26 publicly available GEO and ArrayExpress studies by applying a custom preprocessing pipeline based on GCRMA. The assembled dataset contains 1489 microarray samples of human tissue that measure gene expression of normal lung (NORM) and 5 different lung diseases (lung adenocarcinoma (ADC), lung squamous cell carcinoma (SCC), large cell lung carcinoma (LCLC), asthma (AST), and chronic obstructive pulmonary disease (COPD)) in preparation for subsequent disease classification analysis. The studies included are: GSE994, GSE10072, GSE10245, GSE10445, GSE10799, GSE12345, GSE12667, GSE14814, GSE1643, GSE1650, GSE17475, GSE18842, GSE18965, GSE19188, GSE2109, GSE3141, GSE4302, GSE5058, GSE6253, GSE7368, GSE7670, GSE8545, GSE8581, E-TABM-15, E-MEXP-231, and E-MTAB-47. These studies collected the microarray data using 2 platforms: Affymetrix U133-A (GPL96) and Affymetrix U133-Plus-2 (GPL570).

The following are included in this reanalysis:

79_1 ArrayExpress study E-TABM-15 sample 1, ADC lung surgical resection GPL96
47_1 ArrayExpress study E-TABM-15 sample 2, ADC lung surgical resection GPL96
41_1 ArrayExpress study E-TABM-15 sample 3, ADC lung surgical resection GPL96
61_1 ArrayExpress study E-TABM-15 sample 4, ADC lung surgical resection GPL96
92_1 ArrayExpress study E-TABM-15 sample 5, ADC lung surgical resection GPL96
60_1 ArrayExpress study E-TABM-15 sample 6, ADC lung surgical resection GPL96
86_1 ArrayExpress study E-TABM-15 sample 7, ADC lung surgical resection GPL96
53_1 ArrayExpress study E-TABM-15 sample 8, ADC lung surgical resection GPL96
40_1 ArrayExpress study E-TABM-15 sample 9, ADC lung surgical resection GPL96
33_1 ArrayExpress study E-TABM-15 sample 10, ADC lung surgical resection GPL96
71_1 ArrayExpress study E-TABM-15 sample 11, ADC lung surgical resection GPL96
23_1 ArrayExpress study E-TABM-15 sample 12, ADC lung surgical resection GPL96
78_1 ArrayExpress study E-TABM-15 sample 13, ADC lung surgical resection GPL96
89_1 ArrayExpress study E-TABM-15 sample 14, ADC lung surgical resection GPL96
38_1 ArrayExpress study E-TABM-15 sample 15, ADC lung surgical resection GPL96
84_1 ArrayExpress study E-TABM-15 sample 16, ADC lung surgical resection GPL96
54_1 ArrayExpress study E-TABM-15 sample 17, ADC lung surgical resection GPL96
87_1 ArrayExpress study E-TABM-15 sample 18, ADC lung surgical resection GPL96
59_1 ArrayExpress study E-TABM-15 sample 19, ADC lung surgical resection GPL96
28_1 ArrayExpress study E-TABM-15 sample 20, ADC lung surgical resection GPL96
32_1 ArrayExpress study E-TABM-15 sample 21, ADC lung surgical resection GPL96
67_1 ArrayExpress study E-TABM-15 sample 22, ADC lung surgical resection GPL96
48_1 ArrayExpress study E-TABM-15 sample 23, ADC lung surgical resection GPL96
40_2 ArrayExpress study E-TABM-15 sample 24, NORM lung surgical resection GPL96
33_2 ArrayExpress study E-TABM-15 sample 25, NORM lung surgical resection GPL96
54_2 ArrayExpress study E-TABM-15 sample 26, NORM lung surgical resection GPL96
48_2 ArrayExpress study E-TABM-15 sample 27, NORM lung surgical resection GPL96
84_2 ArrayExpress study E-TABM-15 sample 28, NORM lung surgical resection GPL96
89_2 ArrayExpress study E-TABM-15 sample 29, NORM lung surgical resection GPL96
28_2 ArrayExpress study E-TABM-15 sample 30, NORM lung surgical resection GPL96
41_2 ArrayExpress study E-TABM-15 sample 31, NORM lung surgical resection GPL96
92_2 ArrayExpress study E-TABM-15 sample 32, NORM lung surgical resection GPL96
78_2 ArrayExpress study E-TABM-15 sample 33, NORM lung surgical resection GPL96
87_2 ArrayExpress study E-TABM-15 sample 34, NORM lung surgical resection GPL96
38_2 ArrayExpress study E-TABM-15 sample 35, NORM lung surgical resection GPL96
23_2 ArrayExpress study E-TABM-15 sample 36, NORM lung surgical resection GPL96
61_2 ArrayExpress study E-TABM-15 sample 37, NORM lung surgical resection GPL96
32_2 ArrayExpress study E-TABM-15 sample 38, NORM lung surgical resection GPL96
47_2 ArrayExpress study E-TABM-15 sample 39, NORM lung surgical resection GPL96
79_2 ArrayExpress study E-TABM-15 sample 40, NORM lung surgical resection GPL96
86_2 ArrayExpress study E-TABM-15 sample 41, NORM lung surgical resection GPL96
DL06 ArrayExpress study E-MEXP-231 sample 1, ADC lung surgical resection GPL96
DL01 ArrayExpress study E-MEXP-231 sample 2, ADC lung surgical resection GPL96
DL05 ArrayExpress study E-MEXP-231 sample 3, ADC lung surgical resection GPL96
DL14 ArrayExpress study E-MEXP-231 sample 4, ADC lung surgical resection GPL96
DL39 ArrayExpress study E-MEXP-231 sample 5, ADC lung surgical resection GPL96
DL34 ArrayExpress study E-MEXP-231 sample 6, ADC lung surgical resection GPL96
DL88 ArrayExpress study E-MEXP-231 sample 7, ADC lung surgical resection GPL96
DL09 ArrayExpress study E-MEXP-231 sample 8, ADC lung surgical resection GPL96
DL59 ArrayExpress study E-MEXP-231 sample 9, ADC lung surgical resection GPL96
DL65 ArrayExpress study E-MEXP-231 sample 10, ADC lung surgical resection GPL96
DL31 ArrayExpress study E-MEXP-231 sample 11, ADC lung surgical resection GPL96
DL45 ArrayExpress study E-MEXP-231 sample 12, ADC lung surgical resection GPL96
DL63 ArrayExpress study E-MEXP-231 sample 13, ADC lung surgical resection GPL96
DL36 ArrayExpress study E-MEXP-231 sample 14, ADC lung surgical resection GPL96
DL13 ArrayExpress study E-MEXP-231 sample 15, ADC lung surgical resection GPL96
T42-1 ArrayExpress study E-MEXP-231 sample 16, ADC lung surgical resection GPL96
DL68 ArrayExpress study E-MEXP-231 sample 17, ADC lung surgical resection GPL96
DL50 ArrayExpress study E-MEXP-231 sample 18, ADC lung surgical resection GPL96
DL46 ArrayExpress study E-MEXP-231 sample 19, ADC lung surgical resection GPL96
DL30 ArrayExpress study E-MEXP-231 sample 20, ADC lung surgical resection GPL96
DL40 ArrayExpress study E-MEXP-231 sample 21, ADC lung surgical resection GPL96
DL51 ArrayExpress study E-MEXP-231 sample 22, ADC lung surgical resection GPL96
DL08 ArrayExpress study E-MEXP-231 sample 23, ADC lung surgical resection GPL96
DL35 ArrayExpress study E-MEXP-231 sample 24, ADC lung surgical resection GPL96
DL58 ArrayExpress study E-MEXP-231 sample 25, ADC lung surgical resection GPL96
DL61 ArrayExpress study E-MEXP-231 sample 26, ADC lung surgical resection GPL96
DL33 ArrayExpress study E-MEXP-231 sample 27, ADC lung surgical resection GPL96
DL16 ArrayExpress study E-MEXP-231 sample 28, ADC lung surgical resection GPL96
DL37 ArrayExpress study E-MEXP-231 sample 29, ADC lung surgical resection GPL96
DL12 ArrayExpress study E-MEXP-231 sample 30, ADC lung surgical resection GPL96
DL67 ArrayExpress study E-MEXP-231 sample 31, ADC lung surgical resection GPL96
DL91 ArrayExpress study E-MEXP-231 sample 32, ADC lung surgical resection GPL96
DL54 ArrayExpress study E-MEXP-231 sample 33, ADC lung surgical resection GPL96
DL47 ArrayExpress study E-MEXP-231 sample 34, ADC lung surgical resection GPL96
DL57 ArrayExpress study E-MEXP-231 sample 35, ADC lung surgical resection GPL96
DL03 ArrayExpress study E-MEXP-231 sample 36, ADC lung surgical resection GPL96
DL41 ArrayExpress study E-MEXP-231 sample 37, ADC lung surgical resection GPL96
DL15 ArrayExpress study E-MEXP-231 sample 38, ADC lung surgical resection GPL96
DL66 ArrayExpress study E-MEXP-231 sample 39, ADC lung surgical resection GPL96
DL11 ArrayExpress study E-MEXP-231 sample 40, ADC lung surgical resection GPL96
DL44 ArrayExpress study E-MEXP-231 sample 41, ADC lung surgical resection GPL96
DL38 ArrayExpress study E-MEXP-231 sample 42, ADC lung surgical resection GPL96
DL56 ArrayExpress study E-MEXP-231 sample 43, ADC lung surgical resection GPL96
DL60 ArrayExpress study E-MEXP-231 sample 44, ADC lung surgical resection GPL96
DL48 ArrayExpress study E-MEXP-231 sample 45, ADC lung surgical resection GPL96
DL89 ArrayExpress study E-MEXP-231 sample 46, ADC lung surgical resection GPL96
DL42 ArrayExpress study E-MEXP-231 sample 47, ADC lung surgical resection GPL96
DL32 ArrayExpress study E-MEXP-231 sample 48, ADC lung surgical resection GPL96
DL55 ArrayExpress study E-MEXP-231 sample 49, ADC lung surgical resection GPL96
DL15N ArrayExpress study E-MEXP-231 sample 50, NORM lung surgical resection GPL96
DL50N ArrayExpress study E-MEXP-231 sample 51, NORM lung surgical resection GPL96
DL4_1N ArrayExpress study E-MEXP-231 sample 52, NORM lung surgical resection GPL96
DL4_17N ArrayExpress study E-MEXP-231 sample 53, NORM lung surgical resection GPL96
DL4_7N ArrayExpress study E-MEXP-231 sample 54, NORM lung surgical resection GPL96
DL4_11N ArrayExpress study E-MEXP-231 sample 55, NORM lung surgical resection GPL96
DL86N ArrayExpress study E-MEXP-231 sample 56, NORM lung surgical resection GPL96
DL79N ArrayExpress study E-MEXP-231 sample 57, NORM lung surgical resection GPL96
DL67N ArrayExpress study E-MEXP-231 sample 58, NORM lung surgical resection GPL96
Biopsy_07 ArrayExpress study E-MTAB-47 sample 1, NORM lung surgical resection GPL570
Biopsy_11 ArrayExpress study E-MTAB-47 sample 2, NORM lung surgical resection GPL570
Biopsy_06 ArrayExpress study E-MTAB-47 sample 3, NORM lung surgical resection GPL570
Biopsy_13 ArrayExpress study E-MTAB-47 sample 4, NORM lung surgical resection GPL570
Biopsy_10 ArrayExpress study E-MTAB-47 sample 5, NORM lung surgical resection GPL570
Biopsy_01 ArrayExpress study E-MTAB-47 sample 6, NORM lung surgical resection GPL570
Biopsy_22 ArrayExpress study E-MTAB-47 sample 7, NORM lung surgical resection GPL570
Biopsy_04 ArrayExpress study E-MTAB-47 sample 8, NORM lung surgical resection GPL570
Biopsy_20 ArrayExpress study E-MTAB-47 sample 9, NORM lung surgical resection GPL570
Biopsy_14 ArrayExpress study E-MTAB-47 sample 10, NORM lung surgical resection GPL570
Biopsy_02 ArrayExpress study E-MTAB-47 sample 11, NORM lung surgical resection GPL570
Biopsy_08 ArrayExpress study E-MTAB-47 sample 12, NORM lung surgical resection GPL570

We preprocess using the MATLAB implementation of GCRMA. To minimize preprocessing batch effects, it is desirable to preprocess all samples in the entire dataset together. Preprocessing requires microarray platform-specific chip specifications indicating the locations of each probe on the chip, precluding global preprocessing on meta-analyses that use multiple platforms. To address this problem, we developed and applied a preprocessing pipeline to combine the raw .CEL files from multiple platforms that share the same probe sets. Importantly, our pipeline maps the locations of probes containing identical sequences from the different platforms to enable grouping of these probes and subsequent processing. These "consensus datasets" are then preprocessed normally by applying the GCRMA algorithm. The output of this consensus preprocessing contains only the 22,227 probes that exist on both microarray platforms that we use; probes that only appear on one of the platforms are excluded from preprocessing. We also include "presence/marginal/absence" calls based on the MAS5 protocol, in which the measured values on the "perfect match" (perfectly complementary to target) probes are compared to the values on the "mismatch" (basepair mismatch at position 13 of 25) probes with Wilcoxon signed rank test. "Present" calls are made when the p-value of difference is less than 0.04; "marginal" calls are made when the p-value lies between 0.04 and 0.06, and "absent" calls are made when the p-value is greater than 0.06.
GCRMA signal

Contributor(s)

Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND

Citation(s)

25330348

Submission date

Aug 18, 2014

Last update date

Dec 18, 2014

Contact name

Shuyi Ma

E-mail(s)

[email protected]

Organization name

University of Washington

Department

Department of Pediatrics

Lab

Shuyi Ma Lab

Street address

307 Westlake Avenue North

City

Seattle

State/province

Washington

ZIP/Postal code

98109

Country

USA

Relations

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE60486_normalized.txt.gz	53.7 Mb	(ftp)(http)	TXT
Processed data are available on Series record