Question: DESeq2: interaction term
0
gravatar for salamandra
21 days ago by
salamandra0
salamandra0 wrote:
If we look at the example of Deseq2 vignette on interaction terms:
https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions
Table
   sampleName         fileName genotype condition group
1       AI_s1 A1_ATCACG_counts        I         A    AI
2       AI_s2 A2_TGACCA_counts        I         A    AI
3      AII_s1 A3_CAGATC_counts       II         A   AII
4      AII_s2 A4_TAGCTT_counts       II         A   AII
5     AIII_s1 B1_CGATGT_counts      III         A  AIII
6     AIII_s2 B2_ACAGTG_counts      III         A  AIII
7       BI_s1 B3_ACTTGA_counts        I         B    BI
8       BI_s2 B4_GGCTAC_counts        I         B    BI
9      BII_s1 C1_TTAGGC_counts       II         B   BII
10     BII_s2 C2_GCCAAT_counts       II         B   BII
11    BIII_s1 C3_GATCAG_counts      III         B  BIII
12    BIII_s2 C4_CTTGTA_counts      III         B  BIII

and we do:

dds3 <- DESeqDataSetFromHTSeqCount(sampleTable = Table, design= ~ genotype + condition + genotype:condition)
dds3 <- dds3[rowSums(counts(dds3)) > 1, ]
ddsHTSeq3 <- DESeq(dds3)
resultsNames(ddsHTSeq3)    

[1] "Intercept"              "genotype_II_vs_I"       "genotype_III_vs_I"      "condition_B_vs_A"       "genotypeII.conditionB"  "genotypeIII.conditionB"
results(ddsHTSeq3, name="genotypeII.conditionB")

"genotypeII.conditionB" gives us the difference between the condition effect for a genotype II and the condition effect for the reference genotype I.

But what if we want to know the difference between the genotype effect for conditionB and the genotype effect for the reference condition A? What should we do?

P.S: this is a repost of https://www.biostars.org/p/353618/#356111

deseq2 • 100 views
ADD COMMENTlink modified 17 days ago • written 21 days ago by salamandra0

I’m out of the office for winter break, but will reply when I’m back.

ADD REPLYlink written 21 days ago by Michael Love21k
Answer: C: DESeq2: interaction term
0
gravatar for Kevin Blighe
19 days ago by
Kevin Blighe30
Republic of Ireland
Kevin Blighe30 wrote:

Hey Michael, I had been assisting the user on Biostars: https://www.biostars.org/p/353618/#356111

On more than 1 occasion, I had advised to read the DESeq2 vignette.

salamandra, if you do post on both Biostars and Bioconductor, can you try to indicate this when you re-post? Many users are on both web-sites.

ADD COMMENTlink modified 19 days ago • written 19 days ago by Kevin Blighe30
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