RT @Latrunculia: "This dataset was rarefied to 1,000 sequence reads per sample, representing the lowest sampling effort" Everybody, pleeea…
RT @Latrunculia: "This dataset was rarefied to 1,000 sequence reads per sample, representing the lowest sampling effort" Everybody, pleeea…
RT @Latrunculia: "This dataset was rarefied to 1,000 sequence reads per sample, representing the lowest sampling effort" Everybody, pleeea…
RT @Latrunculia: "This dataset was rarefied to 1,000 sequence reads per sample, representing the lowest sampling effort" Everybody, pleeea…
"This dataset was rarefied to 1,000 sequence reads per sample, representing the lowest sampling effort" Everybody, pleeease, STOP doing this. a typical Illumina sample has ~200 000 reads, why throwing out 99.5% of your data?! https://t.co/yqQGDYgNIB
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible https://t.co/1TzHvzdEfY
@PatSchloss Thanks for this demonstration Pat. What are your thoughts on alternative techniques to rarefaction such as the negative binomial based approaches advocated by McMurdie and Holmes (2014). https://t.co/3csAlM3BDO
@jjminich @BioMickWatson Also, read this paper: https://t.co/patJYGkzQW
RT @YYCist: @BioMickWatson There are alternatives you might want to consider, e.g. https://t.co/4bktwiYoDj
@pathogenomenick @BioMickWatson @SherlockpHolmes Yes, loved this paper! https://t.co/ZtzfmiYkjA
RT @YYCist: @BioMickWatson There are alternatives you might want to consider, e.g. https://t.co/4bktwiYoDj
@BioMickWatson There are alternatives you might want to consider, e.g. https://t.co/4bktwiYoDj
@drob I'm still grumpy about this: https://t.co/ZSqErIfNP6 . It makes some reasonable points, but overstates/oversells. We worked on a response paper for a while but never got it published (or posted to a preprint server ...) https://t.co/pPdbnlPisx
RT @rafaelcuadrat: @BioMickWatson @cabbagesofdoom Actually less and less we are using downsampling/rarefying in microbiome counts data, fav…
@BioMickWatson @cabbagesofdoom Actually less and less we are using downsampling/rarefying in microbiome counts data, favouring more CoDa methods of normalization as CLR, ILR. Some thoughts about that: https://t.co/uaS2eBqsXF
@JWoodelius Thanks so much for this paper and for your insights! I read this paper https://t.co/UoTuyZcEfK and became a bit more hesitant to rarefy. DivNet looks like a great tool!
@KellyBodwin Waste not, Want not: why rarefying microbiome data is inadmissible @SherlockpHolmes @joey711 https://t.co/O8RbaaeYUO
@UrFreundHannah I disagree regarding rarefaction especially concerning alpha metrics. Read this https://t.co/sJs1DsEdKi and also this https://t.co/p1x05XnNSI
@drisso1893 @CalgaroMatteo @LeviWaldron1 @LabRomualdi @nicola_vitulo Looks very interesting. Looking forward to reading more. Very relevant to what McMurdie and Holmes (2014) were exploring in https://t.co/UjojuXV1F7
@paulfharrison https://t.co/ubBnDQUe7u Thoughts?
Am I the only one to think its Fig 1 shows the opposite? Not rarefy increase the chance of false positive, while rarefy reduce it at the cost of lossing stat power. Any thought, folks? Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http
SH: Can model data carefully to produce meaningful estimates of microbiome counts. Points here for an example regarding rarefaction: https://t.co/XYVr9nSS4A
@SherlockpHolmes - wanting not to waste appropriately. in fig2 in https://t.co/6TYIMw7Tcr environment is a clear factor separating all samples; what do you do if you have two factors you think interact, like Location and Time?
RT @JillHagey: @chiranjit_m Hard No. https://t.co/6dYYi0yEch
@chiranjit_m Hard No. https://t.co/6dYYi0yEch
@chiranjit_m How I was taught XD https://t.co/EkCKOr3aGk
RT @raxitdaves: One of my favourite papers https://t.co/P90Ku0dtb0 #ICMR2018
One of my favourite papers https://t.co/P90Ku0dtb0 #ICMR2018
Turns out the answer is just, "cause stats say it's bad." Jokes aside, I'm learning so many good lessons from this class. It's even fostering an appreciation for R I never thought I'd have.
We're talking about McMurdie & Holmes (2014) in my Sequence-based Microbial Community Analysis class today. "Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible". https://t.co/9fcBevmfj1 https://t.co/pNBkSLPwzU
@mike_lustgarten @SherlockpHolmes @ejalm I think Susan's paper on this would be a very good start (and the end maybe :) https://t.co/h0JQhBT3ye
RT @Akis_BeCool: "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible". Are they though? https://t.co/RZ0hOa9rUh
"Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible". Are they though? https://t.co/RZ0hOa9rUh
@LabMutwil @PlantEvolution I don't think there's a single solution; datasets can be highly divergent in composition. DESeq2 provides at least two useful transformation/scaling options (beyond more traditional methods); see https://t.co/itOM54Zjcj and https
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
Just watching this statistician learn how to do statistics from microbial ecologists. I am not sure if it is microbial ecology, or Twitter. https://t.co/uMAvJPycdq
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
@Chowder_Murph @calynum @MarshMicrobe @lab_g0ddess @JoeVineis who wants to present this at lab meeting? https://t.co/qPH6I7UCt0
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
RT @AmyDWillis: Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https:…
Rarefying is statistically illegal. Not adjusting for read count diffs is also illegal. If you haven't already, read https://t.co/llhoJXQNNQ
Microbiome Data를 Rarefying 을 이용해서 표준화하면 안된다는 내용. 많은 사람들이 이 방법을 사용하는데,, Deseq2와 같은 방법을 사용하라고 조언. https://t.co/DY49tzSf8E
RT @gidauria: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible https://t.co/G11NWT9PCM
RT @gidauria: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible https://t.co/G11NWT9PCM
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible https://t.co/G11NWT9PCM
@davisjmcc @mikelove Yup, @joey711 has shown NB good for diff abundance (including w/ DESeq2 or edgeR): https://t.co/2JWKPZV5KB
Susan Holmes: Rarefaction (subsampling to get equal variances btwn samples) is flawed. There's a better way. https://t.co/Aqqk8Q1mhP #JMM17
@SherlockpHolmes https://t.co/jN2Q5lAMn3, https://t.co/Nnsg0VryAl, and the other ET-critical papers that have been pub'd
@snk531 @sydneyglassman I’m happy w/ deseq. Relatedly there’s the argument for no rarefaction at all eg https://t.co/35MwNOOuim
At #PSB16 @SherlockpHolmes: showing paper on using DESeq2 package normally used for RNA-seq for microbiome analysis https://t.co/pQFC1YZb6o
Published in 2014, but just re-read it, includes full R code #bestpractice #PLOSCompBio Rarefying Microbiome Data http://t.co/KgYMrW4iFt
#365papers #Morelike30papers Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible: http://t.co/yIBveUxhve
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/rX5Vb8DJrI
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/rX5Vb8DJrI
Poll: Should you rarefy/normalize NGS data to accout for diff in seq effort among samples? #PLOSCompBio: http://t.co/JF19R4BpN6
Poll: Should you rarefy/normalize NGS data to accout for diff in seq effort among samples? #PLOSCompBio: http://t.co/JF19R4BpN6
Why we should not rarefy anymore? Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/xrzRN0AiZ2
@pdiff1 @Gut_Goddess @daviddespain Is this the reference you were thinking of? "Waste Not, Want Not" @PLOSCompBiol http://t.co/wyfv2Dz6ft
@Gut_Goddess RE: rarefying article mentioned previously. http://t.co/QtX44ZUc8h
@pdiff1 @Gut_Goddess @daviddespain Is this the reference you were thinking of? "Waste Not, Want Not" @PLOSCompBiol http://t.co/wyfv2Dz6ft
Despite its current popularity in microbiome analyses rarefying biological count data is statistically inadmissible http://t.co/TX4lY3mCp2
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/8MlhAJ3SsT
One of my recent favourites: #PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/kklVMkXa9Z
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/G3xSKubSZs
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/G3xSKubSZs
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/G3xSKubSZs
end statement of mcmurdie Thou should not rarefy see http://t.co/p2cTOyvsEv
#PLOSCompBio: Waste Not, Want Not seems to be generating productive discussion about efficient use of data http://t.co/V1PVJGqExM
@merenbey @MikeyJ @joey711 @DrChrisKellogg I agree, Figure 1 is very straight forward http://t.co/kHxoz35A7O
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Debating to rarefy or not bc of http://t.co/Odf49SEKGO, but lecture notes from #edamame2014 convinced me I should keep rarefying for now
Reading: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/zD2ZMUJ4fU #PLOSCompBio #Microbiome
MT @schroed_microbe: "Why Rarefying Microbiome Data Is Inadmissible" http://t.co/bU1CSMqpzb - just shared this with my lab and now.....
"Why Rarefying Microbiome Data Is Inadmissible" http://t.co/SIBHXSIsLE - just shared this with my lab and now everyone's panicking @joey711
"Why Rarefying Microbiome Data Is Inadmissible" http://t.co/SIBHXSIsLE - just shared this with my lab and now everyone's panicking @joey711
To rarefy or not? "Waste not, want not: why rarefying microbiome data is inadmissible." - reviewed@F1000 http://t.co/3InLN2ypFs
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/qtMeDyhf6w
#PLOSCompBio: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/qtMeDyhf6w
@ashley17061 @gilbertjacka Unsure of application for CRTs, but I have been using these methods (http://t.co/3B38dSSNSd) for diff abundance
@pathogenomenick Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible http://t.co/FHVBMAozZ5