User: Axel Klenk
Axel Klenk • 920
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Posts by Axel Klenk
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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 7 weeks 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 7 weeks 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 8 weeks 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 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks 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 10 weeks 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. :-)
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written 10 weeks ago by
Axel Klenk • 920
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... Well, consider the pros and cons: if your screening step is too conservative, you may not have enough candidates for your wet lab experiments and you have a higher risk of missing false negatives. If, OTOH, it is not conservative at all, you may end up with too many candidates for wet lab follow-up ...
written 10 weeks ago by
Axel Klenk • 920
Latest awards to Axel Klenk
Scholar
3 months ago,
created an answer that has been accepted.
For A: Identification of DEGs through limma analysis
Scholar
14 months ago,
created an answer that has been accepted.
For A: Identification of DEGs through limma analysis
Centurion
14 months ago,
created 100 posts.
Supporter
2.5 years ago,
voted at least 25 times.
Teacher
3.6 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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