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jchen1981 / GUniFrac

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please supply a `strata` parameters used example #1

Open qqwxp opened 1 year ago

qqwxp commented 1 year ago

I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After".
The subject-id column name is "Individual".

I excuted the script:

ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, 
                           grp.name = 'Point', feature.dat.type = "proportion",  
                           # Filter to remove rare taxa
                           prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, 
                           # Winsorization to replace outliers
                           is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top',
                           # Posterior sampling will be automatically disabled
                           is.post.sample = FALSE, post.sample.no = 25,            
                           stats.combine.func = max,  
                           # Permutation-based multiple testing correction
                           perm.no = 999,  strata = NULL, 
                           # Reference-based multiple stage normalization
                           ref.pct = 0.5, stage.no = 6, excl.pct = 0.2,
                           # Subjects ID column
                           strata = "Individual",
                           # Family-wise error rate control
                           is.fwer = TRUE, verbose = TRUE, return.feature.dat = T)

however, the error occured:

Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point",  : 
  formal argument "strata" matched by multiple actual arguments

I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right.

jchen1981 commented 1 year ago

It seems you have two “strata” in your args. You need to remove “strata=NULL”Sent from my iPhoneOn Apr 3, 2023, at 10:40 PM, qqwxp @.***> wrote: I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After". The subject-id column name is "Individual". I excuted the script: ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = 'Point', feature.dat.type = "proportion", # Filter to remove rare taxa prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, # Winsorization to replace outliers is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top', # Posterior sampling will be automatically disabled is.post.sample = FALSE, post.sample.no = 25, stats.combine.func = max, # Permutation-based multiple testing correction perm.no = 999, strata = NULL, # Reference-based multiple stage normalization ref.pct = 0.5, stage.no = 6, excl.pct = 0.2, # Subjects ID column strata = "Individual", # Family-wise error rate control is.fwer = TRUE, verbose = TRUE, return.feature.dat = T) however, the error occured: Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point", : formal argument "strata" matched by multiple actual arguments I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right.

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qqwxp commented 1 year ago

It seems you have two “strata” in your args. You need to remove “strata=NULL”Sent from my iPhoneOn Apr 3, 2023, at 10:40 PM, qqwxp @.> wrote: I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After". The subject-id column name is "Individual". I excuted the script: ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = 'Point', feature.dat.type = "proportion", # Filter to remove rare taxa prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, # Winsorization to replace outliers is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top', # Posterior sampling will be automatically disabled is.post.sample = FALSE, post.sample.no = 25, stats.combine.func = max, # Permutation-based multiple testing correction perm.no = 999, strata = NULL, # Reference-based multiple stage normalization ref.pct = 0.5, stage.no = 6, excl.pct = 0.2, # Subjects ID column strata = "Individual", # Family-wise error rate control is.fwer = TRUE, verbose = TRUE, return.feature.dat = T) however, the error occured: Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point", : formal argument "strata" matched by multiple actual arguments I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks a lot...

However, another error occured:

Error in check(sn, control = control, quietly = quietly) : 
  Number of observations and length of Block 'strata' do not match.

I check the source script, and test by give strata the whole variable:

strata <- meta.dat$Individual
Zicoseq(......, strata = strata)

rather than the variable name

Zicoseq(......, strata = "Individual")

to solve this problem

qqwxp commented 1 year ago

Thanks a lot...

However, another error occured:


Error in check(sn, control = control, quietly = quietly) : 

  Number of observations and length of Block 'strata' do not match.

I check the source script, and test by give strata the whole variable:


strata <- meta.dat$Individual

ZicoSeq(......, strata = strata)

rather than the variable name


ZicoSeq(......, strata = "Individual")

to solve this problem

发件人: @. @.> 代表 Chen_LAB 发送时间: 2023年4月4日 11:50 收件人: jchen1981/GUniFrac @.> 抄送: qqwxp @.>; Author @.***> 主题: Re: [jchen1981/GUniFrac] please supply a strata parameters used example (Issue #1)

It seems you have two “strata” in your args. You need to remove “strata=NULL”Sent from my iPhoneOn Apr 3, 2023, at 10:40 PM, qqwxp @. <mailto:@.> > wrote: I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After". The subject-id column name is "Individual". I excuted the script: ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = 'Point', feature.dat.type = "proportion", # Filter to remove rare taxa prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, # Winsorization to replace outliers is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top', # Posterior sampling will be automatically disabled is.post.sample = FALSE, post.sample.no = 25, stats.combine.func = max, # Permutation-based multiple testing correction perm.no = 999, strata = NULL, # Reference-based multiple stage normalization ref.pct = 0.5, stage.no = 6, excl.pct = 0.2, # Subjects ID column strata = "Individual", # Family-wise error rate control is.fwer = TRUE, verbose = TRUE, return.feature.dat = T) however, the error occured: Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point", : formal argument "strata" matched by multiple actual arguments I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right.

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qqwxp commented 1 year ago

It seems you have two “strata” in your args. You need to remove “strata=NULL”Sent from my iPhoneOn Apr 3, 2023, at 10:40 PM, qqwxp @.> wrote: I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After". The subject-id column name is "Individual". I excuted the script: ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = 'Point', feature.dat.type = "proportion", # Filter to remove rare taxa prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, # Winsorization to replace outliers is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top', # Posterior sampling will be automatically disabled is.post.sample = FALSE, post.sample.no = 25, stats.combine.func = max, # Permutation-based multiple testing correction perm.no = 999, strata = NULL, # Reference-based multiple stage normalization ref.pct = 0.5, stage.no = 6, excl.pct = 0.2, # Subjects ID column strata = "Individual", # Family-wise error rate control is.fwer = TRUE, verbose = TRUE, return.feature.dat = T) however, the error occured: Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point", : formal argument "strata" matched by multiple actual arguments I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks a lot...

However, another error occured:

Error in check(sn, control = control, quietly = quietly) : 
  Number of observations and length of Block 'strata' do not match.

I check the source script, and test by give strata the whole variable:

strata <- meta.dat$Individual
ZicoSeq(......, strata = strata)

rather than the variable name

ZicoSeq(......, strata = "Individual")

to solve this problem

jchen1981 commented 1 year ago

Thanks for pointing this out. In the next version, I will use variable name instead.JSent from my iPhoneOn Apr 4, 2023, at 5:10 AM, qqwxp @.***> wrote:

It seems you have two “strata” in your args. You need to remove “strata=NULL”Sent from my iPhoneOn Apr 3, 2023, at 10:40 PM, qqwxp @.> wrote: I want to perform paired samples. The grp.name is "point", which has two labels, i.e. "Before", "After". The subject-id column name is "Individual". I excuted the script: ZicoSeq.obj.p <- ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = 'Point', feature.dat.type = "proportion", # Filter to remove rare taxa prev.filter = 0.2, mean.abund.filter = 0, max.abund.filter = 0.002, min.prop = 0, # Winsorization to replace outliers is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top', # Posterior sampling will be automatically disabled is.post.sample = FALSE, post.sample.no = 25, stats.combine.func = max, # Permutation-based multiple testing correction perm.no = 999, strata = NULL, # Reference-based multiple stage normalization ref.pct = 0.5, stage.no = 6, excl.pct = 0.2, # Subjects ID column strata = "Individual", # Family-wise error rate control is.fwer = TRUE, verbose = TRUE, return.feature.dat = T) however, the error occured: Error in ZicoSeq(meta.dat = meta.dat, feature.dat = comm.p, grp.name = "Point", : formal argument "strata" matched by multiple actual arguments I have check 'Individual' data type (i.e. factor) and its labels. There seems to be all right. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.>

Thanks a lot... However, another error occured: Error in check(sn, control = control, quietly = quietly) : Number of observations and length of Block 'strata' do not match.

I check the source script, and test by give strata the whole variable: strata <- meta.dat$Individual ZicoSeq(......, strata = strata)

rather than the variable name ZicoSeq(......, strata = "Individual")

to solve this problem

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>