UCSF: UCSF
In bhklab/MetaGxBreast: Transcriptomic Breast Cancer Datasets
Description
Format
Details
Source
Description
ExpressionSet for the UCSF Dataset
Format
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experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17428335; http://www.ncbi.nlm.nih.gov/pubmed/?term=14612510
Title:
URL: Not available
PMIDs: 17428335, 14612510
No abstract available.
notes:
summary:
A gene set was identified that correctly predicted outcomes more effective
ly than using histological markers.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe_1 probe_3 ... probe_10365 (8015 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
Details
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assayData: 8015 features, 162 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
29 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
133.00 44.00 11.56 9.25 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
162 character character
alt_sample_name:
Length Class Mode
162 character character
sample_type:
tumor
162
er:
negative positive NA's
41 101 20
pgr:
negative positive NA's
46 94 22
her2:
negative positive NA's
35 19 108
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.800 2.000 2.682 3.200 11.000 7
N:
0 1 NA's
67 82 13
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 44.00 53.00 56.61 70.00 88.00 9
grade:
1 2 3 NA's
14 62 74 12
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 897 2040 2084 2992 8267 29
dmfs_status:
norecurrence recurrence
140 22
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 861 1865 1985 2847 8267 29
recurrence_status:
norecurrence recurrence
125 37
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 1087 2054 2140 3087 8267 29
vital_status:
deceased living NA's
54 99 9
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
31 38 61 22
NA's
10
batch:
UCSF
162
uncurated_author_metadata:
Length Class Mode
162 character character
Source
Not available
bhklab/MetaGxBreast documentation built on April 29, 2021, 5:20 p.m.
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Description Format Details Source
Description
ExpressionSet for the UCSF Dataset
Format
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17428335; http://www.ncbi.nlm.nih.gov/pubmed/?term=14612510
Title:
URL: Not available
PMIDs: 17428335, 14612510
No abstract available.
notes:
summary:
A gene set was identified that correctly predicted outcomes more effective
ly than using histological markers.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe_1 probe_3 ... probe_10365 (8015 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
Details
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | assayData: 8015 features, 162 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
29 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
133.00 44.00 11.56 9.25 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
162 character character
alt_sample_name:
Length Class Mode
162 character character
sample_type:
tumor
162
er:
negative positive NA's
41 101 20
pgr:
negative positive NA's
46 94 22
her2:
negative positive NA's
35 19 108
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.800 2.000 2.682 3.200 11.000 7
N:
0 1 NA's
67 82 13
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 44.00 53.00 56.61 70.00 88.00 9
grade:
1 2 3 NA's
14 62 74 12
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 897 2040 2084 2992 8267 29
dmfs_status:
norecurrence recurrence
140 22
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 861 1865 1985 2847 8267 29
recurrence_status:
norecurrence recurrence
125 37
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 1087 2054 2140 3087 8267 29
vital_status:
deceased living NA's
54 99 9
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
31 38 61 22
NA's
10
batch:
UCSF
162
uncurated_author_metadata:
Length Class Mode
162 character character
|
Source
Not available
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