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Module Generation Description
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Create Analysis
Create Analysis
Analysis Name:
*
(no underscores or periods)
Use Preloaded Data
Upload Data
Microarray Data:
*
Select a sample set
GSE47561_log2_RMA_renormalized_data
CD4+ TIL in human breast cancer - GSE36769.GPL570
GSE36769_CD4+ TIL in human breast cancer - All Samples
GSE36769_CD4+ TIL in human breast cancer
Guy's hospital dataset (GUYT2) - GSE9195.GPL570.fCEL
test_brc_data
test2_brc_data
To delete!-Johannes Gutenberg University (MAINZ) dataset - GSE11121.GPL96
Guys hospital (GUYT) dataset- GSE6532.GPL570
John Radcliff Hospital (OXFU, OXFT) dataset- GSE6532.GPL96
John Radcliff Hospital (OXFU, OXFT) dataset- GSE6532.GPL97
Uppsala and Singapore dataset - GSE4922.GPL96
Uppsala and Singapore dataset - GSE4922.GPL97
Karolinska (STO) dataset - GSE1456.GPL96
Karolinska (STO) dataset - GSE1456.GPL97
Bordet Radcliffe NUH dataset - GSE45255.GPL96
National Cancer Institute – Bari (YAU) dataset - GSE8193.GPL4685
Memorial Sloan-Kettering Cancer Center (MSKCC) dataset - GSE2603.GPL96_Clinical_Samples
University of California San Francisco (YAU) dataset - GSE7378.GPL4685
Guy's hospital dataset (GUYT2) - GSE9195.GPL570
Erasmus Medical Center (EMC) dataset 1 - GSE2034.GPL96
Erasmus Medical Center (EMC) dataset 2 - GSE5327.GPL96
Europe and Cleveland (EMCT) dataset - GSE12093.GPL96
TRANSBIG (TBIG) dataset - GSE7390.GPL96
GSE47561_log2_RMA_2renormalized_data
GSE47561_log2_RMA_5renormalized_data
Memorial Sloan-Kettering Cancer Center (MSKCC) dataset - GSE2603.GPL96 - tissue type-none
Memorial Sloan-Kettering Cancer Center (MSKCC) dataset - GSE2603.GPL96_Clinical samples
Memorial Sloan-Kettering Cancer Center (MSKCC) dataset - GSE2603.GPL96_Breast cancer cell lines
expression.data.combined
expression.data.combined2
BRCA-Adams_DB_Expression.probe_transformed
BRCA-Adams_DB_Expression.probe_transformed2
Nagalla 2013 reconstituted public dataset
Johannes Gutenberg University (MAINZ) dataset - GSE11121.GPL96
Select Group:
*
Select Sample Group:
*
(you can also use the
Annotation Tool
to create a new one )
For a simplified uploading process,
Module Analysis Wizard
will take you through the uploading of data into the Module Analysis Tool step-by-step, and notify you when your analyses are finished.
Microarray Data:
*
Design File:
*
Change default parameters
fields marked with * are required
Preprocessing
Data
Statistical
Perform Quantile Normalization
TRUE
FALSE
Perform Flooring
TRUE
FALSE
Min Expression
Perform Log2
TRUE
FALSE
Perform PALO
TRUE
FALSE
PALX percent
Range Cut
Chip Selection:
Affymetrix: HG-U133A
Affymetrix: HG-U133B
Affymetrix: HG-U133_Plus_2
Illumina: Illumina Hu6 V2
Illumina: Hu6 V2 (Norm.)
Illumina: Hu6 V3
Illumina: Hu V3 Ref 8
Illumina: HT12 V3
Illumina: Hu6 v3 HT12
Illumina: Hu6 V3 (GEO - Raw)
Illumina: HT12 V4
Illumina: Hu8 V2
Illumina: Sentrix Hu-6 v2
Ensembl: RnaSeq1 Hu Ens Gene
Affymetrix: HG 1.0 ST (transcript)
ABI: ABI Human v2
Agilent: Agilent-014850 (feature)
Agilent: Agilent-014850 (probe)
Affymetrix: PrimeView
Affymetrix: Rhesus Macaque
Module Generation:
2
3
Signal pattern:
input type:
BeadStudio
Custom
Metric
zscore
fold
Metric threshold
Intensity Difference Threshold
Measure of center
mean
median
Multiple Testing Correction
TRUE
FALSE
False Discovery Rate
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1.70.7-stable-gxb1-release