search

hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
Other
170 stars 64 forks source link

Differing Results in SCDE Tutorial #69

Closed adamclemmitt closed 5 years ago

adamclemmitt commented 6 years ago

Hi all,

I am a beginner to R and I am currently trying to run the provided SCDE tutorial code in RStudio. I noticed that when I complete the tutorial and load o.ifm directly (using data(o.ifm)), I get results that are fairly close to the example results within the tutorial. However, when I calculate o.ifm with the code provided in the tutorial (using scde.error.models), my answers vary greatly from the example results. I have included the results of both methods below:

Using data(o.ifm):

data o ifm

Using o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 1, threshold.segmentation = TRUE, . . . :

coded_o ifm

Please let me know if you have any idea why this difference is happening, and I apologize if there is an obvious solution to this problem. Thank you in advance for any help!

JEFworks commented 5 years ago

Closing due to issue being duplicated in Google Groups: https://groups.google.com/forum/embed/?place=forum/singlecellstats&showsearch=true&showpopout=true&showtabs=false&parenturl=http%3A%2F%2Fhms-dbmi.github.io%2Fscde%2Fhelp.html#!topic/singlecellstats/GMMDvABvpYA