I’m using DESeq2 for RNA sequencing DGE analysis and I’m having error with this code
dds=DESeqDataSetFromTximport(txi,colData = coldata,design= ~ batch+condition)
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
Here is my coldata
coldata <- read.table(file.path(“Salm_txt_DEseq_update.txt”), header=TRUE)
and I have a column condition with16 rows 12 treated samples and 4 untreated sample
if I remove batch from the chmd line
dds=DESeqDataSetFromTximport(txi,colData = coldata,design=~condition)
it works ok .. but I wish to find out what’s wrong with the batch argument
any help would be appreciated
You’ve described that your file “Salm_txt_DEseq_update.txt” contains a column “condition”. Does that same file contain a column “batch”?
For those coming to this question through search, the problem is probably a missing column “
batch” in the
coldata (“Salm_txt_DEseq_update.txt” in this case) data frame. Variables used in constructing the design formula (
batch in Morris’ example) must refer to columns the dataframe passed as
coldata in the call to
Hi Rob, sorry for the delay
yes my file now contains a column “batch” and the error is fixed but I can’t see variation after adding batch, which probably is due to
a mistake for using this command.
I have 4 different conditions (A,B,C,D), and for each condition I have two samples, there is a batch effect only in one condition (D) so, should I use a different
argument of batch for only this two samples (D)?
for example, here is the batch column of the data frame: