Dear Kevin,
thanks for your fast reply and sorry for the maybe confusing description.
Lets assume I have the following raw read counts of six mouse RNA-Seq samples in two conditions (lets say 'control' and 'treated', 3 replicates each), so a table like this:
|
control_rep1 |
control_rep2 |
control_rep3 |
treated_rep1 |
treated_rep2 |
treated_rep3 |
ENSMUSG00000000001 |
6000 |
5754 |
6116 |
5560 |
5083 |
4952 |
ENSMUSG00000000003 |
0 |
0 |
0 |
0 |
0 |
0 |
ENSMUSG00000000028 |
868 |
881 |
844 |
952 |
840 |
818 |
that I can feed (together with information about the conditions, ...) into a DESeqDataSet
which is a subclass of SummarizedExperiment
, as you already mentioned.
From this DESeqDataSet
I can run the DESeq()
function to obtain again a DESeqDataSet
including all of my input features by row and my samples by column, with the (normalized) expression values of each feature in each sample. If I understood you correctly, I should use this data matrix in the exprs
slot of the ExpressionSet
object.
Then I think I also need to build up an AnnotatedDataFrame
holding each of my six samples by row and containing additional phenotypic information (for the phenodata
slot of ExpressionSet
). So regarding to the manual it would be enough to define two columns 'Treatment' and 'Timepoint' maybe like this:
|
Treatment |
Timepoint |
control_rep1 |
control |
0 |
control_rep2 |
control |
0 |
control_rep3 |
control |
0 |
treated_rep1 |
treated |
0 |
treated_rep2 |
treated |
0 |
treated_rep3 |
treated |
0 |
So, if I understood this correctly until this point, I should be able to create a ExpressionSet
object from this data and then put this into
GO_results <- GO_analyse(eSet = MyCustomizedSet, f = "Treatment")
Thanks for your help,
Martin
EDIT: since our last posts were somehow overlapping: yes, thanks for the information up to this point, I think I understand now what kind of data objects I have to prepare and will give it a try
Glad to hear it Martin,
Could you please close this discussion by "accepting" the answer? Just to show how that the issue was resolved, if future users come around.
As I understand, there should be a button available for you to click, as you are the person who created this discussion.
Thanks!