User: Guido Hooiveld
Guido Hooiveld • 2.1k
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Posts by Guido Hooiveld
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... As is nicely phrased in e.g. this paper:
"... SVs can be regressed out of the data to obtain “cleaned” data for visualization (as we do in this report), however differential expression statistics should not be performed on this “clean” data, as this too can lead to anti-conservative bias resulting ...
written 6 days ago by
Guido Hooiveld • 2.1k
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Answer:
C: MA plot in R
... Did you already check the help pages?
> library(limma)
> ?plotWithHighlights()
Then see:
status: character vector giving the control status of each point, of same length as x and y. If NULL, then all points are plotted in the background color, symbol and size.
values: character vector gi ...
written 6 days ago by
Guido Hooiveld • 2.1k
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... In the few cases I need to visualize the 'cleaned' data I use the approaches mentioned in the Biostars thread (AFAIK they are the same). However, if you would like to identify differentially expressed genes, you should take these into account as covariates in your (linear) model rather than to use t ...
written 6 days ago by
Guido Hooiveld • 2.1k
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... Could it be Rtools is not (properly) installed? See my updated answer above. Otherwise I don't know...
...
written 20 days ago by
Guido Hooiveld • 2.1k
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... BTW, i noticed you are using the development version of Bioconductor (i.e. v3.6), whereas below I use the release version (v3.5)... Maybe for BioC-development the procedure is different?
...
written 20 days ago by
Guido Hooiveld • 2.1k
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... Works fine for me: I started a fresh R-session, then 1st installed the library GenomeInfoDbData, followed by installation of dada2.
Please notice that i did not provide the argument dep=T with biocLite().
While being on Windows, I also had Rtools installed before starting R (because GenomeInfoDbDat ...
written 20 days ago by
Guido Hooiveld • 2.1k
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... It is working! But, please note:
According to James: "... so I have added code to both the release and devel version of AnnotationDbi to do this for the arabidopsis chips as well."
The current release version of BioC is version 3.5, to be used with R version 3.4.0. See here.
You are using R vers ...
written 20 days ago by
Guido Hooiveld • 2.1k
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... It is working for me!?!
I downloaded all 99 (compressed) CEL files from the GEO experiment you mentioned (GSE14578), loaded them all into R, and then performed gcRMA normalization. As said before, without any problems.
The only things I can suggest is that:
- start a fresh R session (because I no ...
written 24 days ago by
Guido Hooiveld • 2.1k
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... Mmm, you don't provide much info for anyone to help troubleshooting..... First of all, which type of array do you want to normalize? Also, please show the full code you used as well as output from sessionInfo().
<<EDIT>> As can be seen in my (first) comment below, your code is workin ...
written 24 days ago by
Guido Hooiveld • 2.1k
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... Yes, you can build yourselves an OrgDb for Tetrahymena thermophile using the function makeOrgPackageFromNCBI() from the library AnnotationForge. You will only need the taxonomy ID of T. Thermophile, which apparently is 312017. Please note that this OrgDb contains (only) the annotation information av ...
written 24 days ago by
Guido Hooiveld • 2.1k
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For A: Taking surrogate variable into account before running PCA
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For A: Taking surrogate variable into account before running PCA
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For LIMMA: warning coercing argument of type 'double' to logical
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