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| Status |
Public on May 25, 2022 |
| Title |
ISPY2_672734 |
| Sample type |
RNA |
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| Source name |
Breast cancer biopsy (pre-treatment)
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| Organism |
Homo sapiens |
| Characteristics |
patient id: 672734
tissue: Breast cancer biopsy (pre-treatment)
hr: 1
her2: 0
mp: 1
pcr: 0
arm: Paclitaxel + Ganitumab
adjustment method: ComBat Adjust
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was performed by Agendia Inc (Irvine, CA).
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| Label |
Cy3
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| Label protocol |
Labeling was performed by Agendia Inc (Irvine, CA).
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| Hybridization protocol |
Hybridization was performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL30494 (updated version of GPL16233).
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| Scan protocol |
Scanning was performed by Agendia Inc (Irvine, CA).
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| Data processing |
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).
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| Submission date |
Jan 19, 2022 |
| Last update date |
May 25, 2022 |
| Contact name |
Denise M Wolf |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, San Francisco
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| Street address |
2340 Sutter st
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL30493 |
| Series (2) |
| GSE194040 |
I-SPY2-990 mRNA/RPPA Data Resource: mRNA component |
| GSE196096 |
I-SPY2-990 mRNA/RPPA Data Resource |
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| Relations |
| Reanalysis of |
GSM5481200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5826554_ISPY2_672734_GPL16233_SingleChannel_FullGenome+.txt.gz |
653.9 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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