Question: rlog not found
0
gravatar for crowsreign42
18 months ago by
crowsreign420 wrote:
Hi! I am trying to do PCA which uses DESeq2. I installed the package directly from Bioconductor, and but when running the script, I get an error that the function rlog() couldn't be found. What should I do?
Thank you in advance
rlog rlog transformation • 472 views
ADD COMMENTlink written 18 months ago by crowsreign420

You should copy/paste the code you used, along with the error, as well as the output from sessionInfo().

But do note that any time R says a function can't be found, it's because you either haven't installed or loaded the package that contains that function.

ADD REPLYlink written 18 months ago by James W. MacDonald51k

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
library(DESeq2)

rld = rlog(samples, blind=TRUE)

Output: Error in rlog(samples, blind = TRUE) : could not find function "rlog"

ADD REPLYlink written 18 months ago by crowsreign420

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_2.14.1       S4Vectors_0.18.1     BiocGenerics_0.26.0  BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.0  tools_3.5.0     RCurl_1.95-4.10 bitops_1.0-6   
 

ADD REPLYlink written 18 months ago by crowsreign420

Note that DESeq2 isn't loaded.

ADD REPLYlink written 18 months ago by Michael Love26k

What can I do to load it?

ADD REPLYlink written 18 months ago by crowsreign420

Shouldn't it work with the following commands?

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
library(DESeq2)

ADD REPLYlink written 18 months ago by crowsreign420

You tell me. Do you get an error when you run library(DESeq2) ?

ADD REPLYlink written 18 months ago by Michael Love26k

I also have the same problem. This is the output I get:

> library(DESeq2)
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded

 

But I don't know how to fix it

ADD REPLYlink written 18 months ago by itsits010

Perhaps you installed R-3.5.0 and copied over packages installed from a previous version?
 

ADD REPLYlink written 18 months ago by Peter Langfelder2.3k

If that is the case do you know what can I do to fix it?

ADD REPLYlink written 18 months ago by itsits010

First question is, did you (or whoever installed R) copy the packages over? R does not copy packages from older installations by itself.

The safest way to fix a broken installation is to uninstall R, remove your personal library (which is usually the culprit) - your personal R library usually sits in the first folder returned by .libPaths() - then reinstall R and reinstall all packages.

ADD REPLYlink written 18 months ago by Peter Langfelder2.3k

The GenomeInfoDb package doesn't currently have a Windows binary version. You can either wait for that to get fixed, or you can install the Rtools and then you will be able to compile yourself.

ADD REPLYlink written 18 months ago by James W. MacDonald51k

Hmm.. there seems to be one on the package page https://www.bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html - or am I missing something?

ADD REPLYlink written 18 months ago by Peter Langfelder2.3k

Both BiocParallel and GenomeInfoDb were missing the win binaries earlier today.

ADD REPLYlink written 18 months ago by James W. MacDonald51k

Well, that was a quick fix! So the OP should be able to install GenomeInfoDb and try again, and if that doesn't work, I would reinstall everything.

ADD REPLYlink written 18 months ago by Peter Langfelder2.3k
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