Question about multi-factor Deseq analysis
1
0
Entering edit mode
FaisalH • 0
@faisalh-18189
Last seen 6.0 years ago

Hi there!

I would like to use DESeq2 for microbiome data to investigate gene abundance on different groups.

To make it simple, this is information about my samples. I have 2 main groups of patient. 1- with disease 2-matched control to each sample. I have 2 samples for each patient at 2 time-points (TP). 

I'm trying to run deseq2 to investigate the gene differential expression between two time-points of groups with disease and control. Then between same time-point between disease and control group. This picture should make the analysis strategy more clearer https://www.dropbox.com/s/ee7gsb21rx9ge81/Screenshot%202018-11-05%2016.21.34.png?dl=0 

I split my data to 4 groups. 1- Disease group: First and last TP, 2- Control groups: First and last TP, 3- First TP: Disease and control, and 4- Last TP: Disease and control groups.

I have 2 columns in my metadata/factor table. First coldata Group::First and Last. Second column Condition and each 2 samples from one paitient paired in one number. For example, each sample at Early collection and Late collection from one patient given one number.

This is the design I used for my model

AllData$Group <- factor(AllData$Group)
AllData$Condition <- factor(AllData$Condition)

dds <- DESeqDataSetFromMatrix(countData = GenesCount,
                              colData = AllData,
                              design= ~ Group + Condition)


dds<-DESeq(dds)

design(dds) <- formula(~ Group + Condition)

dds <- DESeq(dds, betaPrior=FALSE)

 

However, when I run the first group pf data of Disease group for both Early and Late collection samples I got this for resultsNames(dds)

 resultsNames(dds)
 [1] "Intercept"              "Group_Disease_Late_vs_Disease_Early" "Condition_2_vs_1"       "Condition_3_vs_1"       "Condition_4_vs_1"      
 [6] "Condition_5_vs_1"       "Condition_6_vs_1"       "Condition_7_vs_1"       "Condition_8_vs_1"       "Condition_9_vs_1"      
[11] "Condition_10_vs_1"      "Condition_11_vs_1"      "Condition_12_vs_1"      "Condition_13_vs_1"      "Condition_14_vs_1"     
[16] "Condition_15_vs_1"     

 

I believe this analysis compare every paired samples to the first paired number 1 ! which look strange for me.

I am wondering is my model for this experiment is correct ?  any advice to improve the analysis methodology?

Thank you!

DESeq deseq2 microbiome gut microbiome • 1.2k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

Your description of the design sounds exactly like something explained in the vignette:

https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#group-specific-condition-effects-individuals-nested-within-groups

Can you take a look at this section first?

ADD COMMENT

Login before adding your answer.

Traffic: 834 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6