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bioinformatics-core-shared-training / rnaseq-pipeline

A Short Course on the interpretation of results from the CRUK-CI rna-seq pipeline
https://bioinformatics-core-shared-training.github.io/rnaseq-pipeline
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Adding an extra column removed lines #6

Open pajanne opened 7 years ago

pajanne commented 7 years ago

5: Cleaned dataset 30,086 lines

Compute on data 5 26,586 lines

using Compute an expression on every row tool and expression c7<0.05

strange...

markdunning commented 7 years ago

it is because of the NA values in the adjusted p-value column

deTable <- read.csv("t47d_Treatment_DEA_Prog-vs-Control_all.csv") table(is.na(deTable$padj))

FALSE TRUE 26586 3500

Possibly we could filter out the NA values, but I couldn't see a way to do that in Galaxy yet

pajanne commented 7 years ago

Well, they seems to be filered out anyway then when you do the compute but the cleaned dataset still have them. If the column has 'NA' we could use the filter tool c1=NA?