User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk920
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920
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Location:
Switzerland
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6 hours ago
Joined:
9 years, 8 months ago
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a*********@idorsia.com

Posts by Axel Klenk

<prev • 124 results • page 1 of 13 • next >
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Comment: C: DESeq2 I installed from latest Bionconductor version is still old version
... 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 Klenk920
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Answer: A: DESeq2 I installed from latest Bionconductor version is still old version
... 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 Klenk920
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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 Klenk920
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Comment: C: getGEO function doesn't download the expression data
... 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 Klenk920
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Answer: A: getGEO function doesn't download the expression data
... 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 Klenk920
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Answer: A: How do I stop DESeq2 from loading and additional errors related to the package.
... (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 Klenk920
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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 Klenk920
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Comment: C: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... 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 Klenk920
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Comment: C: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... 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 10 weeks ago by Axel Klenk920
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Comment: C: Possible ways to select differential expressed genes using DeSeq2 or edgeR
... 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 Klenk920

Latest awards to Axel Klenk

Scholar 3 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Limma un moderated t-test
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.
Scholar 14 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 2.5 years ago, created an answer that has been accepted. For A: Limma un moderated t-test
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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