Question

DESeq not showing all coefficient

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Jitendra ▴ 10

@nabiyogesh-11718

Last seen 6 months ago

United Kingdom

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:

geno_stage_LRPR_15D_vs_HRPR_15D
geno_stage_LRPR_0D_vs_HRPR_0D


resultsNames(dds)
>      [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 • 1.1k views

ADD COMMENT • link updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by Jitendra ▴ 10

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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:

geno_stage_HRPR_12D_vs_HRPR_0D

Thanks

ADD REPLY • link 5.6 years ago Jitendra ▴ 10

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

ADD REPLY • link 5.6 years ago Michael Love 43k

score 0 · Answer 1 · 2019-05-13

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Michael Love 43k

@mikelove

Last seen 10 days ago

United States

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 COMMENT • link 5.6 years ago Michael Love 43k

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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 REPLY • link 5.6 years ago Jitendra ▴ 10

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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 REPLY • link 5.6 years ago Michael Love 43k