search

joey711 / shiny-phyloseq

An interactive web application for demonstrating and using phyloseq.
http://joey711.github.io/shiny-phyloseq
GNU General Public License v3.0
60 stars 45 forks source link

Rlog transformation #65

Open lisamctaggart opened 8 years ago

lisamctaggart commented 8 years ago

The Rlog transformation does not seem to work, although the other transformations work.

Under d3Network it says: Error: 'data' must be of a vector type, was 'NULL'

Underordination it says: Error: arguments imply differing number of rows: 0, 1

Any thoughts?

joey711 commented 8 years ago

Can you share a MRE and version/system information?

lisamctaggart commented 8 years ago

Sorry, what is an MRE?

Here is the System information and versions:

OS Name Microsoft Windows 7 Enterprise Version 6.1.7601 Service Pack 1 Build 7601 Other OS Description Not Available OS Manufacturer Microsoft Corporation System Name OND2C00872906 System Manufacturer Hewlett-Packard System Model HP Compaq Pro 6300 MT System Type X86-based PC Processor Intel(R) Core(TM) i3-2120 CPU @ 3.30GHz, 3300 Mhz, 2 Core(s), 4 Logical Processor(s) BIOS Version/Date Hewlett-Packard K01 v02.86, 05/06/2013 SMBIOS Version 2.7 Windows Directory C:\windows System Directory C:\windows\system32 Boot Device \Device\HarddiskVolume1 Locale Canada Hardware Abstraction Layer Version = "6.1.7601.17514" User Name OAHPP\lisa.mctaggart Time Zone Eastern Daylight Time Installed Physical Memory (RAM) 4.00 GB Total Physical Memory 3.48 GB Available Physical Memory 1.14 GB Total Virtual Memory 6.95 GB Available Virtual Memory 4.13 GB Page File Space 3.48 GB Page File C:\pagefile.sys

packageVersion("phyloseq") [1] ‘1.14.0’ packageVersion("DESeq2") [1] ‘1.10.1’ packageVersion("ggplot2") [1] ‘2.1.0’ packageVersion("scales") [1] ‘0.4.0’ packageVersion("grid") [1] ‘3.2.5’ packageVersion("shiny") [1] ‘0.13.2’ packageVersion("shinythemes") [1] ‘1.0.1’ packageVersion("networkD3") [1] ‘0.2.10’ packageVersion("gridExtra") [1] ‘2.2.1’ packageVersion("png") [1] ‘0.1.7’ packageVersion("markdown") [1] ‘0.7.7’ From: Paul J. McMurdie [mailto:notifications@github.com] Sent: May-03-16 3:34 PM To: joey711/shiny-phyloseq Cc: Lisa McTaggart; Author Subject: Re: [joey711/shiny-phyloseq] Rlog transformation (#65)

Can you share a MRE and version/system information?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/joey711/shiny-phyloseq/issues/65#issuecomment-216640624

lisamctaggart commented 8 years ago

Attached is an MRE.

Thanks, Lisa

From: Paul J. McMurdie [mailto:notifications@github.com] Sent: May-03-16 3:34 PM To: joey711/shiny-phyloseq Cc: Lisa McTaggart; Author Subject: Re: [joey711/shiny-phyloseq] Rlog transformation (#65)

Can you share a MRE and version/system information?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/joey711/shiny-phyloseq/issues/65#issuecomment-216640624

joey711 commented 8 years ago

I couldn't see package information, etc., but I'll update dependency requirements very soon, basically as soon as the BioC release happens later today...

joey711 commented 8 years ago

Also, I can't "see" your attachment. Where is your MRE?

lisamctaggart commented 8 years ago

Here is the MRE. Please see attached.

From: Paul J. McMurdie [mailto:notifications@github.com] Sent: May-04-16 1:20 PM To: joey711/shiny-phyloseq Cc: Lisa McTaggart; Author Subject: Re: [joey711/shiny-phyloseq] Rlog transformation (#65)

Also, I can't "see" your attachment. Where is your MRE?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/joey711/shiny-phyloseq/issues/65#issuecomment-216937836

joey711 commented 8 years ago

Please go here for posting and you'll understand why I can't see it...

https://github.com/joey711/shiny-phyloseq/issues/65

please post a URL, code, instructions, etc...