Tutorial_1_start
Created: 2014-04-16 14:54:09
This partial workflow is the starting point for Taverna tutorial held at the Leiden University Medical Center on April 17, 2014.
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Authors (1)
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Titles (1)
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Descriptions (1)
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| Fetch and combine transcriptomics and proteomics data from NSC11 cells in
GEO and PRIDE respectively. Apply spectral counting on the proteomics data.
This workflow is for tutorial/educational use only. The cells were not grown
under the same conditions, nor should raw spectral counts be used for protein
quantitation. |
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Dependencies (0)
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Inputs (0)
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Processors (4)
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| Name |
Type |
Description |
| Transcriptomics_Data |
stringconstant |
Valuehttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSM1098404&id=13672&db=GeoDb_blob95 |
| Proteomics_Data |
stringconstant |
Valuehttp://www.ebi.ac.uk/pride/archive/files/21260108 |
| Import_into_R_and_Plot |
rshell |
Scriptcombined_data<-in1;
A<-matrix(unlist(strsplit(combined_data,"\t")), nrow = length(combined_data), ncol = 4, byrow = TRUE);
genes<-as.numeric(A[,3]);
proteins<-as.numeric(A[,4]);
png(filename="comparison.png", height=400, width=400, bg="white");
plot(genes, proteins, xlab="gene expression", ylab="protein spectral count");
dev.off();
R Serverlocalhost:6311 |
| SpreadsheetImport |
spreadsheet |
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Beanshells (0)
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Outputs (3)
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| Name |
Description |
| proteins |
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| genes |
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| comparison |
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Datalinks (4)
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| Source |
Sink |
| Transcriptomics_Data:value |
SpreadsheetImport:fileurl |
| Import_into_R_and_Plot:proteins |
proteins |
| Import_into_R_and_Plot:genes |
genes |
| Import_into_R_and_Plot:comparison |
comparison |
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