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Old 05-15-2014, 06:20 AM   #21
Kwasi
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Hi Mike,

Everything worked like a charm! Thank you for the very prompt response.

Cheers,
Kwasi

Last edited by Kwasi; 05-15-2014 at 06:20 AM. Reason: spelling error
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Old 06-05-2014, 07:26 AM   #22
sridharacharya
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I faced the same problem with plotMA of the DESeq2 package.
The command gives error
Error in as.vector(data):
no method for coercing this S4 class to a vector


I checked the input data to be of the correct format. Then later I realized that this was caused due to the limma library that was loaded. I was using limma to make other graphs, which I am doing much later in the script. However, I loaded limma library along with DESeq2 library at the start of the script.

When I removed limma library from the start of the script and placed it exactly where it was needed (much later than the plotMA commands), then the problem with plotMA vanished. Obviously both packages offer this command and there seem to be differences in the input formats. In the case when I got the error, the command was defaulting to the limma package which was the reason for the error.
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Old 06-05-2014, 07:42 AM   #23
Michael Love
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hi thanks for the note sridharacharya. I think you can also specify
Code:
DESeq2::plotMA
.
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Old 10-22-2014, 10:27 AM   #24
Golsheed
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Hi Michael,

I'm sort of having the same problem. I upgraded to R 3.1.1 and then installed DESeq2 1.6.1. When installing DESeq2, I got the warning that it couldn't upgrade 3 packages including MASS. Afterwards, running the normalizationFactors script resulted in the following error:

> normalizationFactors(dds) <- NF
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘normalizationFactors<-’ for signature ‘"DESeqDataSet", "data.frame"’

Following the suggestions on http://bioconductor.org/install/#upd...uctor-packages then (as per your suggestion), I recompiled all the Bioconductor packages, which at the end gave me the following warnings:

Warning messages:
1: packages ‘manipulate’, ‘rstudio’, ‘base’, ‘compiler’, ‘datasets’, ‘graphics’, ‘grDevices’, ‘grid’, ‘methods’, ‘parallel’, ‘splines’, ‘stats’, ‘stats4’, ‘tcltk’, ‘tools’, ‘utils’ are not available (for R version 3.1.1)
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘MASS’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘DESeq2’ had non-zero exit status

So at least the list of faulty packages was reduced to only MASS (from the 3 packages I mentioned above) and DESeq2. Here's the session info:
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=fr_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=fr_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_CA.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BiocInstaller_1.16.0

loaded via a namespace (and not attached):
[1] BiocGenerics_0.12.0 GenomeInfoDb_1.2.0 IRanges_2.0.0
[4] parallel_3.1.1 S4Vectors_0.4.0 stats4_3.1.1
[7] tools_3.1.1 XVector_0.6.0

At that point, I tried removing DESeq2 and reinstalling it manually, which as was sort of expected incurred the following errors:

mv: cannot move `/home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/DESeq2' to `/home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/00LOCK-DESeq2/DESeq2': Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NAMESPACE to /home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/DESeq2/NAMESPACE: Permission denied
Warning in file.copy(f, instdir, TRUE) :
problem copying ./NEWS to /home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/DESeq2/NEWS: Permission denied
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file '/home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/DESeq2/DESCRIPTION': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘DESeq2’
* removing ‘/home/golsheed/R/x86_64-pc-linux-gnu-library/3.1/DESeq2’

The downloaded source packages are in
‘/tmp/RtmpMfeWZz/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘DESeq2’ had non-zero exit status

I'd greatly appreciate any input or comment, if you could please think of any.

Thanks,
Golsheed
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Old 10-22-2014, 10:33 AM   #25
Michael Love
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Hmm, you should back up a bit. Basically, there's never a good reason to install Bioc package manually, you will just end up with a headache of incompatible packages.

I don't think there was any installation error.

If you lookup the help for the function you got an error with...

?normalizationFactors

Code:
normalizationFactors(object, ...) <- value

object a DESeqDataSet object.

value the matrix of normalization factors
...'value' should be a matrix.
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Old 10-22-2014, 10:40 AM   #26
Golsheed
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Thanks a lot for the help, it works!

Golsheed
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Old 10-22-2014, 10:42 AM   #27
Golsheed
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Thanks a lot for the help, it works!

Golsheed
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Old 10-27-2014, 02:13 PM   #28
Golsheed
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Default Nested Mixed Model in DESeq2

Hi,

I was wondering whether I could use a nested mixed model in DESeq2? Specifically, the model I have in mind has two fixed effects A and B, and a random effect C nested in B. I was wondering whether the following could work?
design = ~ A + B + (1| C %in% B)
I'd appreciate any help or comment.

Thanks,
Golsheed


Quote:
Originally Posted by Michael Love View Post
Hmm, you should back up a bit. Basically, there's never a good reason to install Bioc package manually, you will just end up with a headache of incompatible packages.

I don't think there was any installation error.

If you lookup the help for the function you got an error with...

?normalizationFactors

Code:
normalizationFactors(object, ...) <- value

object a DESeqDataSet object.

value the matrix of normalization factors
...'value' should be a matrix.
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Old 10-27-2014, 02:18 PM   #29
Michael Love
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it's best to make a new post for a different topic, rather than add on to a thread which is about something else.
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