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I have a treatment and control in two time points like this

> design
                                               condition time
    Sample_Sample_1_3x_CTRL_MSC_24_hrs_replicate1    control   24
    Sample_Sample_2_3x_CTRL_MSC_24_hrs_replicate1    control   24
    Sample_Sample_3_3x_CTRL_MSC_24_hrs_replicate1    control   24
    Sample_Sample_10_3x_CTRL_MSC_48_hrs_replicate1   control   48
    Sample_Sample_11_3x_CTRL_MSC_48_hrs_replicate1   control   48
    Sample_Sample_12_3x_CTRL_MSC_48_hrs_replicate1   control   48
    Sample_Sample_4_3x_IT_MSC_24_hrs_replicate1           IT   24
    Sample_Sample_5_3x_IT_MSC_24_hrs_replicate1           IT   24
    Sample_Sample_6_3x_IT_MSC_24_hrs_replicate1           IT   24
    Sample_Sample_13_3x_IT_MSC_48_hrs_replicate1          IT   48
    Sample_Sample_14_3x_IT_MSC_48_hrs_replicate1          IT   48
    Sample_Sample_15_3x_IT_MSC_48_hrs_replicate1          IT   48
    > 

I want to test between between treatment and control considering time point 24 hours to 48 hours

I have done like this

dds <- DESeqDataSetFromMatrix(countData=a,colData=design, design=~time + condition + time:condition)

ddsTC <- DESeq(dds, test="LRT", reduced = ~ time + time:condition)

> resultsNames(ddsTC)
[1] "Intercept"                "condition_IT_vs_control"  
[3] "time"                     "conditionIT.time" 

 

What is the difference of the results of these codes

results(ddsTC, name="condition_IT_vs_control", test="Wald")

versus

results(ddsTC, name="conditionIT.time", test="Wald")

Actually I want to know what condition_IT_vs_control gives and what conditionIT.time gives

Thank you so much for any intuition

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condition_IT_vs_control gives the effect of condition, conditionIT.time is the interaction of condition and time. If you wanted to test the effect of time, use name="time".

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  • $\begingroup$ Thank you, using which contrast I can get the difference of IT versus control but considering time goes from 24 hours to 48 hours? $\endgroup$
    – Exhausted
    Oct 19 at 16:35
  • $\begingroup$ Just condition_IT_vs_control, since time is compensated for by fitting all coefficients at the same time (let me know if that phrasing is confusing). $\endgroup$
    – Devon Ryan
    Oct 19 at 19:22

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