Question: Bringing in data for DESeq2, can't match first column colData to column names of countData
0
3 months ago by
ishtarredman0 wrote:

Hi, Im new to using bioconductor packages in R, I'm importing .csv files into R for DeSeq2 analysis but I can't seem to get the first column of my colData to match the column names of my countData.

The match (vector 1, vector 2) function isn't working and I think it has to do with the layout of my data.

The image on the left is my table and the one on the right is an example of the required format. I need my 'column 0' (the one with the blue arrow) to contain the EnsembleIDs i.e the ENSG000..instead of the numbers 1,2,3,4,... Any help as to how to change to format of the dataframe ?

deseq2 bioconductor • 97 views
modified 3 months ago by Michael Love24k • written 3 months ago by ishtarredman0
Answer: Bringing in data for DESeq2, can't match first column colData to column names of
1
3 months ago by
Michael Love24k
United States
Michael Love24k wrote:

I can't see the image, can you just post the head(counts) and head(colData)?

The easiest approach would be to construct or order the colData manually so that it matches the counts.

What I recommend in the workflow is to build the counts matrix using the colData, e.g. reading in quantification or count files using a column of colData directly.