I am running DESeq2 for paired analysis of subjects under different conditions, but get

Error in checkFullRank(modelMatrix) : the model matrix is not full rank

when I run

dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ Subject + Condition)

My colData is below:

                 Subject    Condition

170.HF.HP_S33   subject170  CHD.HF.HP

172.HF.HP_S10   subject172  CHD.HF.HP

92.HF.HP_S38    subject92   CHD.HF.HP

170.HF.LP_S32   subject170  CHD.HF.LP

172.HF.LP_S45   subject172  CHD.HF.LP

92.HF.LP_S37    subject92   CHD.HF.LP

170.LF.HP_S31   subject170  CHD.LF.HP

172.LF.HP_S11   subject172  CHD.LF.HP

92.LF.HP_S36    subject92   CHD.LF.HP

170.LF.LP_S30   subject170  CHD.LF.LP

172.LF.LP_S12   subject172  CHD.LF.LP

92.LF.LP_S35    subject92   CHD.LF.LP

170.Static_S29  subject170  CHD.Static

172.Static_S13  subject172  CHD.Static

92.Static_S34   subject92   CHD.Static

107.HF.HP_S5    subject107  FD.HF.HP

112.HF.HP_S43   subject112  FD.HF.HP

116.HF.HP_S18   subject116  FD.HF.HP

107.HF.LP_S7    subject107  FD.HF.LP

112.HF.LP_S42   subject112  FD.HF.LP

116.HF.LP_S17   subject116  FD.HF.LP

107.LF.HP_S6    subject107  FD.LF.HP

112.LF.HP_S41   subject112  FD.LF.HP

116.LF.HP_S16   subject116  FD.LF.HP

107.LF.LP_S8    subject107  FD.LF.LP

112.LF.LP_S40   subject112  FD.LF.LP

116.LF.LP_S15   subject116  FD.LF.LP

107.Static_S9   subject107  FD.Static

112.Static_S39  subject112  FD.Static

116.Static_S14  subject116  FD.Static

105.HF.HP_S28   subject105  IPAH.HF.HP

168.HF.HP_S23   subject168  IPAH.HF.HP

95.HF.HP_S1     subject95   IPAH.HF.HP

105.HF.LP_S27   subject105  IPAH.HF.LP

168.HF.LP_S22   subject168  IPAH.HF.LP

95.HF.LP_S44    subject95   IPAH.HF.LP

105.LF.HP_S26   subject105  IPAH.LF.HP

168.LF.HP_S21   subject168  IPAH.LF.HP

95.LF.HP_S2     subject95   IPAH.LF.HP

105.LF.LP_S25   subject105  IPAH.LF.LP

168.LF.LP_S20   subject168  IPAH.LF.LP

95.LF.LP_S3     subject95   IPAH.LF.LP

105.Static_S24  subject105  IPAH.Static

168.Static_S19  subject168  IPAH.Static

95.Static_S4    subject95   IPAH.Static

I would like to perform paired comparison for subjects between two given conditions, so for example, subjects 170, 172, 92 in condition CHD.HF.HP vs. condition CHD.HF.LP. When I limit the colData to just the above example (three subjects compared between two conditions), I don't get an error, but when expanding it to all conditions and samples as reflected in the full colData, I get the model matrix error.

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6

Thanks for your help!

We have a section of the vignette on how to setup designs with individuals are nested within groups.

Beyond reading that, I'd recommend for setting up an appropriate design to consult with a local statistician or someone familiar with linear models in R.