Question: STATegRa Minimum number of samples
0
gravatar for Lluís Revilla Sancho
18 months ago by
European Union
Lluís Revilla Sancho480 wrote:

I observed that the function omicsCompAnalysis fails with less than 9 samples.

Is this a hard requirement or is due to some particularity of my data?

With the same code I got several errors with different subsets of the same data:

subscript out of bounds
arguments imply differing number of rows: 4, 6, 2
argument of length 0
arguments imply differing number of rows: 0, 8

As with these arguments it works depending on the subset I suspect there is something else but I can't figure out what.

Many thanks,

Lluís

Code used, where keep is what is changing for to select a subset of data:


tryCatch({cc <- selectCommonComps(t(otus_i[keep, ]), t(otus_s[keep, ]), Rmax = 3)
  PCA.selection(t(otus_i[keep, ]), fac.sel = "single%", varthreshold = 0.03)$numComps
  PCA.selection(t(otus_s[keep, ]), fac.sel = "single%", varthreshold = 0.03)$numComps
  (ms <- modelSelection(list(eS_i, eS_s), Rmax = 7, fac.sel = "single%",
                        varthreshold = 0.03))

  # grid.arrange(cc$pssq, cc$pratios, ncol=2)
  # Omics Integration
  discoRes <- omicsCompAnalysis(list("Intestinal" = eS_i, "Stools" = eS_s), 
                                Names = c("Intestinal", "Stools"),
                                method = "DISCOSCA",
                                Rcommon = ms$common,
                                Rspecific = ms$dist,
                                center = TRUE, scale = TRUE)
  plotVAF(discoRes, main = colnames(keepCol)[i])
  }, error = function(e){message(e)})

I am using the latest R 3.4.2 version and the latest Bioconductor version 3.6.

stategra • 262 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Lluís Revilla Sancho480

Reproducible example? Code that you used to produce the error? 

ADD REPLYlink written 18 months ago by Sean Davis21k

I can't reproduce the error without data, I can't reproduce the error with the vignette data and I won't post online my data, but I updated to include the relevant part of the code.

ADD REPLYlink written 18 months ago by Lluís Revilla Sancho480
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 337 users visited in the last hour