User: Axel Klenk
Axel Klenk • 920
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Posts by Axel Klenk
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... Wild guess (as you don't say where your data come from): some Agilent microarrays contain 10 copies of a subset of their oligos.
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written 20 days ago by
Axel Klenk • 920
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... The first link points to a mirror (or rather: archive) of BioC release 3.0 -- with two releases per year, this is now more than three years old.
Note that the current version is really 1.20 (twenty!) and not 1.2.0 and hence a lot newer than 1.4 or 1.6. If you check the PDF from your second link you ...
written 3 months ago by
Axel Klenk • 920
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... There is nothing to fix.
In the Bioconductor release version 3.7 DESeq2 is in fact at version 1.20.0:
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
so that's correct. The current devel version (to be released with BioC 3.8 in fall) is at 1.21.10:
https://bioconductor.org/packa ...
written 3 months ago by
Axel Klenk • 920
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Comment:
C: Installation path not writable
... This message is about updating packages 'foreign' and 'survival', not 'pathview' or other BioC packages. These two packages come with the R installation and you need to run R as an administrator in order to update them.
If there are no other complaints by biocLite() -- have you tried loading 'pathv ...
written 3 months ago by
Axel Klenk • 920
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... I can reproduce this behaviour when I have pkg rlang attached and can see it in your sessionInfo() as well. rlang masks exprs(). The easiest way to get around this problem is to use
> str(Biobase::exprs(gse[[1]]))
Does that work for you?
...
written 4 months ago by
Axel Klenk • 920
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... See the Value: section of ?getGEO : it returns a list of ExpressionSet objects, not an ExpressionSet object.
Hence, you want:
> str(exprs(gse[[1]]))
Hope this helps.
...
written 4 months ago by
Axel Klenk • 920
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... (Hmmm... not sure what happened to my previous answer. Anyway:)
No, DESeq2 is not normally loaded on R startup. I think this could be an issue with your RStudio project or R may restore a previously saved worksapce on startup that contains a DESeq2 object. The latter can be avoided by starting R li ...
written 4 months ago by
Axel Klenk • 920
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Answer:
A: Why some packages don't work?
... Apparently the installation failed. What is the output from your biocLite("affydata") ?
...
written 4 months ago by
Axel Klenk • 920
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... Good.
1) I cannot tell only form the PCA plot.
2) Have a look at Bioc pkg sva. Try finding surrogate variables in your data (see the vignette). If you find one that you're confident is a batch effect, you can try removing it using sva or combat (same pkg). Or, in case you want to use limma for dif ...
written 4 months ago by
Axel Klenk • 920
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... Yes, as a consequence of independent filtering some padj are NA, so you need
> write.csv(as.data.frame(res[!is.na(res$padj) & res$padj < 0.1 & res$log2FoldChange > log2(1.5),]), file="DEGs.csv")
Hope this will work. :-)
...
written 4 months ago by
Axel Klenk • 920
Latest awards to Axel Klenk
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For Download problem with GEOquery::getGEO()
Scholar
5 months ago,
created an answer that has been accepted.
For A: Identification of DEGs through limma analysis
Scholar
16 months ago,
created an answer that has been accepted.
For A: Identification of DEGs through limma analysis
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16 months ago,
created 100 posts.
Supporter
2.7 years ago,
voted at least 25 times.
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3.8 years ago,
created an answer with at least 3 up-votes.
For A: basic R question: concatenate two numeric vectors grouped by element index
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