Hi there,

I'm hoping to get some help with the design table for my analysis, I continue to get the model.matrix error when I put it into DESeq2 and I'm not sure how to resolve this. Below, I have included an example of my design table. Pooled and multiplexed sequencing used - there was a total of 5 Pools and within each pool 24 index's used for multiplexing. Would I be correct in saying the pools are equivalent to batches? Are samples that are from the same individual, that match in Tissue and core, sequenced across 2 pools technical replicates? Further, are samples from the same individual that are the same tissue type (e.g. Tumour) but derived from different core technical replicates or biological? I would like to model the effect If any running samples in different pools are. Each person had 5-10 cores.

Note. Sample names in the following format, ID_poolNumber

Sample        ID    Pool     Tissue        Core
id1_pool1      1      1        Tumour        1
id1_pool2      1      2        Tumour        1
id1_pool3      1      3        Tumour        4
id2_pool1      2      1        Benign        3
id2_pool1      2      1        Benign        1
id3_pool1      3      1        Tumour        1
id3_pool1      3      1        Tumour        1
id3_pool1      3      1        Benign        2

Any advice would be great