Rlog transformation

[lisamctaggart]

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]

Can you share a MRE and version/system information?

[lisamctaggart]

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:[email protected]]
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//issues/65#issuecomment-216640624

[lisamctaggart]

Attached is an MRE.

Thanks,
Lisa

From: Paul J. McMurdie [mailto:[email protected]]
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//issues/65#issuecomment-216640624

[joey711]

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]

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

[lisamctaggart]

Here is the MRE. Please see attached.

From: Paul J. McMurdie [mailto:[email protected]]
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//issues/65#issuecomment-216937836

[joey711]

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

#65

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