paired analysis using metagenomeSeq
3
0
Entering edit mode
manasishah86 ▴ 30
@manasishah86-11034
Last seen 8.1 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)

Thanks for your time,

Best,

Manasi

metagenomeseq logfc paired samples standard error • 2.7k views
ADD COMMENT
0
Entering edit mode
@joseph-nathaniel-paulson-6442
Last seen 7.5 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
ADD COMMENT
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

ADD REPLY
0
Entering edit mode

In the meantime, I'd recommend using fitZig.

ADD REPLY
0
Entering edit mode
@atekurrahman48-11511
Last seen 8.1 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.

At last, and I feel this is the most critical, is security. I have heard issues around there with pretty much every email administration supplier EXCEPT, trust it or not, AOL. I have, in every one of my years of utilizing AOL, never had an issue with security as to their product or email itself. I can't say that for different suppliers, without saying any names. I'm certain you yourself have heard the frightfulness stories of certain email administration suppliers being hacked. Just as of late, a companion of mine had her email hacked (won't say the supplier's name) that practically cost me $2,470. I'll abandon it at that mailing list.

So as should be obvious, there is nobody answer to this inquiry. You need to experience every one of the choices and pick the give that you believe is best for you. By considering conveyance, usefulness and security, in the long run you'll make the privilege decision.To YOUR Success,Steven Wagenheim

Tired of not getting your messages conveyed, read or opened? Tired of not making any deals from your email advertising endeavors? Visit my site at

ADD COMMENT
0
Entering edit mode
@mariamake0011-11514
Last seen 8.1 years ago

Eight Tips on Keeping Your Email Lists Clean and to Increase Subscriber Response

Every internet marketer will be proud to tell how big their list is. 80,000 subscribers... 200,000 subscribers... But how much response they will be getting if they sent an email campaign? Its not the number of emails you have in the database. Its the quality of the list. The more squeaky clean your list is, more profits you will get. Here are some tips to maintain your list quality: 1. Use double opt-in. This way you can make sure that email is valid. The software you are using should be able to send a confirmation message, so subscriber will click on it to confirm their subscription. Simply buy email database defined as sending solicited email to your opt-in list. Webmasters has to keep a form on their websit(s). Prospects if they want to receive email from that webmaster, they will enter their name and email address to subscribe. This in-house built list is safest to do email marketing with. How to get them sign up? Buy a mailing list manager software. Create a mailing list there. Copy and paste the html code on your website. Use double opt-in. Means subscribers has to click on the link provided to them in their initial email. 2. Deal with Bounces mercilessly. Delete bounces... period. But make sure its a hard bounce. Hard bounce is when recipient mail server rejects your email. Soft bounce is when your email accepted by recipient's mail server but bounced back because of reasons like mail box is full, your message is large than receiving mail server upper limit etc. Make sure to configure your list manager to try to send the messages few times before you delete the email addresses. 3. Try to avoid free email accounts. Its a little hard to implement. Because now a days most people use a free email account like hotmail, yahoo.com though they have their own domains. This is because they don't want to expose themselves or they might be affraid that publisher of the list might send junk or spam to them. So think of pros and cons the situation and follow this tip. 4. Provide an option for subscribers to change their email address. Some list management software or services provide a link to your subscriber details and lists he opted for. From there he can change his email address. This way its easy for them to update their profile. 5. Validating the domain. While accepting an email address in to your database make the list manager to validate it either by some javascript or other means. 6. Delete unsubscribers. ALWAYS include an unsubscribe link for easy unsubscriptions. Once in a while do a search for unsubscribers and delete them from your database. 7. DON'T buy email lists. Not a good experience with buying email lists. Most of them sell email addresses that they will get from website email extractors. If you see an offer like one million emails for $19.95... Simply turned down that offer. You will feel glad about it if you gain some experince in internet marketing. 8. Manual import of subscribers. If you got your subscribers from your old list manager to new one or from your helpdesk to your mailing list manager etc, be careful to avoid spelling errors.

ADD COMMENT

Login before adding your answer.

Traffic: 712 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