Closed jjgao closed 4 years ago
_sequenced
is used in code)cases_sequenced.txt
and cases_cnaseq.txt
on datahub@rmadupuri asked if we should use "Samples with..." instead of "Tumors with...". I think it's a good idea.
+1
On Feb 25, 2019, at 11:03 AM, JianJiong Gao notifications@github.com wrote:
@rmadupuri https://github.com/rmadupuri asked if we should use "Samples with..." instead of "Tumors with...". I think it's a good idea.
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@jjgao @schultzn @ritikakundra here is the table of current case_list_names and their normalized values. Could you let me know if the normalized names are correct or require any changes? Thank you!
case file name | current case_list_name | new normalized case_list_name |
---|---|---|
cases_all.txt | All tumors | All samples |
cases_sequenced.txt | Sequenced Tumors / Sequenced Samples / All Seq Tumors / All sequenced samples / All Sequenced Tumors | Samples with mutation data |
cases_cna.txt | Tumor Samples with CNA data / Tumors CNA | Samples with CNA data |
cases_cnaseq.txt | Tumor Samples with sequencing and CNA data / Tumors with sequencing and CNA data | Samples with mutation and CNA data |
cases_log2CNA.txt | Tumor Samples with log2 copy-number / Tumors log2 copy-number | Samples with log2 copy-number |
cases_methylation_all.txt | All tumor samples with methylation data | All samples with methylation data |
cases_methylation_hm27.txt | Tumor Samples with methylation data (HM27) / Tumors with methylation data | Samples with methylation data (HM27) |
cases_methylation_hm450.txt | Tumor Samples with methylation data (HM450) / Tumors with methylation data (HM450) | Samples with methylation data (HM450) |
cases_miRNA.txt | Tumor Samples with microRNA data (microRNA-Seq) / Tumors with microRNA | Samples with microRNA data (microRNA-Seq) |
cases_mRNA_U133.txt | Tumor Samples with mRNA data (U133 microarray only) | Samples with mRNA data (U133 microarray only) |
cases_mRNA.txt | Tumor Samples with mRNA data (Agilent microarray) / Tumors with mRNA | Samples with mRNA data (Agilent microarray) |
cases_protein_quantification.txt | Tumor Samples with Protein Quantification (Mass Spec) / Protein Quantification (Mass Spec) | Samples with Protein Quantification (Mass Spec) |
cases_RNA_Seq_mRNA.txt | Tumor Samples with mRNA data (RNA Seq) / Tumors with mRNA data (RNA Seq) | Samples with mRNA data (RNA Seq) |
cases_RNA_Seq_v2_mRNA.txt | Tumor Samples with mRNA data (RNA Seq V2) / Tumors with mRNA data (RNA Seq V2) | Samples with mRNA data (RNA Seq V2) |
cases_rppa.txt | Tumor Samples with RPPA data / Tumors with RPPA data | Samples with RPPA data |
Thanks. See my edits in red below.
Niki.
On Feb 25, 2019, at 4:34 PM, Ramya Madupuri notifications@github.com wrote:
@jjgao https://github.com/jjgao @schultzn https://github.com/schultzn @ritikakundra https://github.com/ritikakundra here is the table of current case_list_names and their normalized values. Could you let me know if the normalized names are correct or require any changes? Thank you!
case file name current case_list_name new normalized case_list_name cases_all.txt All tumors All samples cases_sequenced.txt Sequenced Tumors / Sequenced Samples / All Seq Tumors / All sequenced samples / All Sequenced Tumors Samples with mutation data cases_cna.txt Tumor Samples with CNA data / Tumors CNA Samples with CNA data cases_cnaseq.txt Tumor Samples with sequencing and CNA data / Tumors with sequencing and CNA data Samples with mutation and CNA data cases_log2CNA.txt Tumor Samples with log2 copy-number / Tumors log2 copy-number Samples with log2 copy-number data cases_methylation_all.txt All tumor samples with methylation data All Samples with methylation data cases_methylation_hm27.txt Tumor Samples with methylation data (HM27) / Tumors with methylation data Samples with methylation data (HM27) cases_methylation_hm450.txt Tumor Samples with methylation data (HM450) / Tumors with methylation data (HM450) Samples with methylation data (HM450) cases_miRNA.txt Tumor Samples with microRNA data (microRNA-Seq) / Tumors with microRNA Samples with microRNA data (microRNA-Seq) cases_mRNA_U133.txt Tumor Samples with mRNA data (U133 microarray only) Samples with mRNA data (U133 microarray only) cases_mRNA.txt Tumor Samples with mRNA data (Agilent microarray) / Tumors with mRNA Samples with mRNA data (Agilent microarray) cases_protein_quantification.txt Tumor Samples with Protein Quantification (Mass Spec) / Protein Quantification (Mass Spec) Samples with protein Quantification data (Mass Spec) cases_RNA_Seq_mRNA.txt Tumor Samples with mRNA data (RNA Seq) / Tumors with mRNA data (RNA Seq) Samples with mRNA data (RNA Seq) cases_RNA_Seq_v2_mRNA.txt Tumor Samples with mRNA data (RNA Seq V2) / Tumors with mRNA data (RNA Seq V2) Samples with mRNA data (RNA Seq V2) cases_rppa.txt Tumor Samples with RPPA data / Tumors with RPPA data Samples with protein RPPA data (RPPA) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/datahub/issues/444#issuecomment-467192577, or mute the thread https://github.com/notifications/unsubscribe-auth/ALV34FXy-yPAwc1kAZxsvH217eUOL9O7ks5vRFb7gaJpZM4YTChZ.
Edits did not come through. Here is an image.
Summary table of normalized case list names and descriptions - (for reference)
case list file | normalized name | normalized description |
---|---|---|
cases_all.txt | All samples | All samples (# samples) |
cases_sequenced.txt | Samples with mutation data | Samples with mutation data (# samples) |
cases_cna.txt | Samples with CNA data | Samples with CNA data (# samples) |
cases_cnaseq.txt | Samples with mutation and CNA data | Samples with mutation and CNA data (# samples) |
cases_log2CNA.txt | Samples with log2 copy-number data | Samples with log2 copy-number data (# samples) |
cases_methylation_all.txt | Samples with methylation data | Samples with methylation data (# samples) |
cases_methylation_hm27.txt | Samples with methylation data (HM27) | Samples with methylation (HM27) data (# samples) |
cases_methylation_hm450.txt | Samples with methylation data (HM450) | Samples with methylation (HM450) data (# samples) |
cases_miRNA.txt | Samples with microRNA data (microRNA-Seq) | Samples with microRNA data (# samples) |
cases_mRNA_U133.txt | Samples with mRNA data (U133 microarray) | Samples with mRNA expression data (# samples) |
cases_mRNA.txt | Samples with mRNA data (Agilent microarray) | Samples with mRNA expression data (# samples) |
cases_protein_quantification.txt | Samples with protein data (Mass Spec) | Samples with protein data (Mass Spec) (# samples) |
cases_RNA_Seq_mRNA.txt | Samples with mRNA data (RNA Seq) | Samples with mRNA expression data (# samples) |
cases_RNA_Seq_v2_mRNA.txt | Samples with mRNA data (RNA Seq V2) | Samples with mRNA expression data (# samples) |
cases_rppa.txt | Samples with protein data (RPPA) | Samples protein data (RPPA) (# samples) |
cases_complete.txt | Complete samples | Samples with mutation, CNA and expression data (# samples) |
@jjgao @schultzn Do we want to rename these case lists as well? They are only used in the poetic study:
cases_methylation_promoters_hmEPIC.txt cases_methylation_genebodies_hmEPIC.txt cases_methylation_promoters_wgbs.txt cases_methylation_genebodies_wgbs.txt
And this one in gbm_tcga only: cases_GSVA.txt
@yichaoS I think these are fine.
@schultzn commented on Fri Oct 19 2018
The term sequenced tumors is misleading. To be consistent with what we use in the study view, we should rename these lists to:
"Tumors with mutation data" and "Tumors with mutation and CNA data"