Question: DESeq not showing all coefficient
gravatar for nabiyogesh
6 weeks ago by
nabiyogesh0 wrote:

Hi, here resultNames(adds) is not showing all the coefficient, could you please suggest me how I can view all the comparison. There are two genotypes (HRPR AND LRPR ) and 0DAYS, 3, 6, 9, 12, 15, 18, 24, 27, TOTAL 9 DEVELOPMENT STAGES. Here I group STAGE AND GENOTYPES together as factor and use geno_stage as design. It is not showing coeffiect like:


>      [1] "Intercept"                      "geno_stage_HRPR_12D_vs_HRPR_0D"
>      [3] "geno_stage_HRPR_15D_vs_HRPR_0D" "geno_stage_HRPR_18D_vs_HRPR_0D"
>      [5] "geno_stage_HRPR_24D_vs_HRPR_0D" "geno_stage_HRPR_27D_vs_HRPR_0D"
>      [7] "geno_stage_HRPR_3D_vs_HRPR_0D"  "geno_stage_HRPR_6D_vs_HRPR_0D" 
>      [9] "geno_stage_HRPR_9D_vs_HRPR_0D"  "geno_stage_LRPR_0D_vs_HRPR_0D" 
>     [11] "geno_stage_LRPR_12D_vs_HRPR_0D" "geno_stage_LRPR_15D_vs_HRPR_0D"
>     [13] "geno_stage_LRPR_18D_vs_HRPR_0D" "geno_stage_LRPR_24D_vs_HRPR_0D"
>     [15] "geno_stage_LRPR_27D_vs_HRPR_0D" "geno_stage_LRPR_3D_vs_HRPR_0D" 
>     [17] "geno_stage_LRPR_6D_vs_HRPR_0D"  "geno_stage_LRPR_9D_vs_HRPR_0D"
deseq2 • 91 views
ADD COMMENTlink modified 6 weeks ago by Michael Love24k • written 6 weeks ago by nabiyogesh0

Dear Michael,

could you please confirm me in above comparison which is act as a reference. How the reference is decided in these cases where we group two variable.

If extract two fold up and down log2fold change result from the below code then what does it mean:



ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by nabiyogesh0

Take a look at the vignette and the workflow for beginners. The meaning of the LFC is explained in detail.

ADD REPLYlink written 5 weeks ago by Michael Love24k
Answer: DESeq not showing all coefficient
gravatar for Michael Love
6 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

It only prints the names of the coefficients, but you can contrast various levels using

results(dds, contrast=c("...","...","..."))

See the help page for ?results or the vignette for details.

ADD COMMENTlink written 6 weeks ago by Michael Love24k

Thank a lot, Michael.

I do have one more query:

To extract differential expressed genes which output we used from below these two command:

**res <- results(dds, name="condition_trt_vs_untrt")**
# or to shrink log fold changes association with condition:
**res <- lfcShrink(dds, coef="condition_trt_vs_untrt", type="apeglm")**

In vignette it is mention that lfcShrink is need for plotting and gene rank: could you please exactly tell me which plotting and where do we need gene rank when we only need to report differential gene expression based on fold change and Padj value.

I am little bit confused, I hope you got my point.

Kind Regards Yogesh

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by nabiyogesh0

You don't need shrunken LFC to report DE genes, e.g. DESeq2 genes with FDR < X.

We find them useful for providing the LFC, which moderates overly large LFC. You can again consult the vignette for details on the shrunken LFC, or see the publications to get some motivation on why we developed these methods.

ADD REPLYlink written 6 weeks ago by Michael Love24k
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