Entering edit mode
4.9 years ago
Bioinfonext
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460
Hi
I have imported phyloseq object into metagenomeSeq, I do have three treatment group:T1, T2 and T3. I want to see how these treatment group affect the microbial diversity in plant roots.
I want to do pairwise comparison, T1_VS_T2 , T2_VS_T3 and T1_VS_T3. I have tried below code to extract T1_vS_T2, IS IT CORRECT?
here I use the code but need some correction:
> root_data <- phyloseq_to_metagenomeSeq(root_M_filter)
**DO I need to used normalize count for further processing? what is setting?
> normalizedMatrix <- MRcounts(root_data, norm = TRUE)
> settings = zigControl(maxit = 1, verbose = FALSE)
> mod = model.matrix(~root_data$Treatment)
> colnames(mod) = levels(root_data$Treatment)
> res = fitZig(obj = root_data, mod = mod, control = settings)
> res
An object of class "fitZigResults"
Slot "fit":
An object of class "MArrayLM"
$coefficients
T1 T2 T3
71f84e7910006f22684121564206e8ca -2.8129112 -0.321366092 0.06113294
54e204fb99c80764e964456dadd6a0e5 0.5643061 0.019018800 1.01351768
55cd1fc570879d645bbf7a3642e9b0a8 -3.1159264 0.072348076 0.02205983
65f5c31e12c277aec319e2096463f9d2 -0.1355134 -0.004567206 0.53119153
7bed62f0fef250fd831dcf13bf43f4fc 1.9469670 -0.596315540 -0.35124338
scalingFactor
71f84e7910006f22684121564206e8ca 1.62101725
54e204fb99c80764e964456dadd6a0e5 -0.24292482
55cd1fc570879d645bbf7a3642e9b0a8 1.50462644
65f5c31e12c277aec319e2096463f9d2 0.05833637
7bed62f0fef250fd831dcf13bf43f4fc -0.56247683
> finalMod = slot(res, "fit")$design
> contrast.matrix = makeContrasts(T1 - T2, levels = finalMod)
> fit2 = contrasts.fit(zigFit, contrast.matrix)
> fit2 = eBayes(fit2)
> topTable(fit2)
logFC AveExpr t P.Value
3147790f0d5a78316fb9dd64f53b9473 11.262064 14.091887 16.331949 3.482815e-15
d2ec9f3b77975c0f457e4b7413b217ff 9.466087 12.212476 10.606122 6.159311e-11
7b908379d1fd2e75d84fd9aaecfd3f77 6.907182 9.784971 9.163780 1.267984e-09
d5fdc1df6dfd31acce9a34b9d8a76590 5.404459 8.373729 7.035926 1.802316e-07
19ddf8e59673c884734cf6093c672da0 5.381863 8.449413 7.011910 1.912363e-07
Kind Regards