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/joey711/shiny-phyloseq/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/joey711/shiny-phyloseq/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/joey711/shiny-phyloseq/issues/65#issuecomment-216937836

[joey711]

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...