paired analysis using metagenomeSeq
3
0
Entering edit mode
manasishah86 ▴ 30
@manasishah86-11034
Last seen 6.0 years ago

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)

Best,

Manasi

metagenomeseq logfc paired samples standard error • 1.6k views
0
Entering edit mode
@joseph-nathaniel-paulson-6442
Last seen 5.5 years ago
United States
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
0
Entering edit mode

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

0
Entering edit mode

In the meantime, I'd recommend using fitZig.

0
Entering edit mode
@atekurrahman48-11511
Last seen 6.0 years ago

A typical inquiry that is regularly asked by Internet advertisers who do email promoting or simply utilize email a considerable measure in their showcasing endeavors is it accurate to say that this is one..."What's the best email administration supplier to utilize?" Well, wouldn't life be incredible if there was only one response to that? Tragically, as with everything else in life, the answer relies on upon what it is you're hoping to escape your email administration supplier. This article clarifies usa email list.

There is no doubt that the quantity of email administration suppliers is amazing without a doubt. Off the highest point of my head you have Google Gmail, Yahoo, AOL, Hotmail, USA Mail, without any end in sight and on. To test every one of them out would actually take you a month of Sundays. What do you do on the off chance that you don't have that much time and would prefer not to take a risk that you'll settle on the wrong decision? All things considered, here are a couple tips.

At the highest priority on the rundown is conveyance. The amount of your email are you really going to get OR is it going to wind up in your spam box or worse...not conveyed by any means. For instance, as an AOL client, among numerous other email administration suppliers that I utilize, I know beyond all doubt that if AOL sees a specific number of spam messages originating from a specific area, or even suspect they're spam, they will basically not convey messages from that space. I know this on the grounds that there are huge amounts of messages I hope to get from specific individuals that never get to my AOL account. For those messages, I need to depend on one of my different records.

Something else that may be essential to you is usefulness. For instance, Gmail has some truly cool components where you can have every email go to a specific organizer relying upon who the email is from. This is something that you don't get with AOL and I am going to figure, a considerable lot of the other email administration suppliers also. Indeed, from the general population I've addressed on this subject, Gmail is by all accounts the supplier of decision among as parcel of them.