Question: paired analysis using metagenomeSeq
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gravatar for manasishah86
2.6 years ago by
manasishah8630
manasishah8630 wrote:

Can we use the fitFeatureModel function in metagenomeSeq to determine log fold changes adjusting for paired samples i.e for example tumor and  tumor adjacent biopsy microbiome samples? i.e in the tutorial can we add a pair factor that denotes samples from the same host as P1, P2 and so on in the model matrix?

  mod <- model.matrix(˜1 + PairFactor+ SmokingStatus , data = pd)

lungres1 = fitFeatureModel(lungData, mod)

Thanks for your time,

Best,

Manasi

ADD COMMENTlink modified 2.6 years ago by mariamake00110 • written 2.6 years ago by manasishah8630
Answer: paired analysis using metagenomeSeq
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gravatar for Joseph Nathaniel Paulson
2.6 years ago by
United States
Joseph Nathaniel Paulson270 wrote:
Not right now, but yes - very soon. On 2016-09-19 19:13, manasishah86 [bioc] wrote: > Activity on a post you are following on support.bioconductor.org [1] > > User manasishah86 [2] wrote Question: paired analysis using metagenomeSeq [3]: > > Can we use the fitFeatureModel function in metagenomeSeq to determine log fold changes adjusting for paired samples i.e for example tumor and tumor adjacent biopsy microbiome samples? i.e in the tutorial can we add a pair factor that denotes samples from the same host as P1, P2 and so on in the model matrix? > > mod <- model.matrix(˜1 + PairFactor+ SmokingStatus , data = pd) > > lungres1 = fitFeatureModel(lungData, mod) > > Thanks for your time, > > Best, > > Manasi > ------------------------- > > Post tags: metagenomeseq, logfc, paired samples, standard error > > You may reply via email or visit paired analysis using metagenomeSeq Links: ------ [1] https://support.bioconductor.org [2] manasishah86 [3] paired analysis using metagenomeSeq
ADD COMMENTlink written 2.6 years ago by Joseph Nathaniel Paulson270

Thanks Joe, what alternative would you suggest for in the meanwhile? An option that outputs standard error. The topTable function in limma+voom though extremely fast, do not provide standard errors

-Manasi

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by manasishah8630

In the meantime, I'd recommend using fitZig.

ADD REPLYlink written 2.6 years ago by Joseph Nathaniel Paulson270
Answer: paired analysis using metagenomeSeq
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gravatar for atekurrahman48
2.6 years ago by
atekurrahman480 wrote:

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ADD COMMENTlink written 2.6 years ago by atekurrahman480
Answer: paired analysis using metagenomeSeq
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gravatar for mariamake0011
2.6 years ago by
mariamake00110 wrote:

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ADD COMMENTlink written 2.6 years ago by mariamake00110
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