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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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Issue with the data? #201

Closed HAFSAKHAN9 closed 1 year ago

HAFSAKHAN9 commented 1 year ago

Step 1 of 7: Checking data... Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function '%in%': dim(X) must have a positive length. I have small set of data, 4 samples. I have repeatedly checked the data, it is correct. what am I doing wrong? switchAnalyzeRlist <- importRdata( isoformCountMatrix = "fpkm_matrix.txt", designMatrix = "design_matrix.txt", isoformExonAnnoation = "annotation.gtf" ) design_Matrix.txt fpkm_matrix.txt

emmafjones commented 1 year ago

your column names for isoformCountMatrix need to exactly match the sample IDs, so I would try removing FPKM from the column names or adding the FPKM prefix to your sampleIDs in the design matrix.

kvittingseerup commented 1 year ago

You are giving strings as input instead of the actual data 🙂