User: Axel Klenk

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Axel Klenk • 920
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Switzerland
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Posts by Axel Klenk

<prev • 125 results • page 1 of 13 • next >
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Answer: A: genes repeated in the heatmap several times(10x) when using limma
... Wild guess (as you don't say where your data come from): some Agilent microarrays contain 10 copies of a subset of their oligos. ...
written 12 weeks ago by Axel Klenk • 920
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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 6 months ago by Axel Klenk • 920
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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 6 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 6 months ago by Axel Klenk • 920
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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 6 months ago by Axel Klenk • 920
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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 6 months ago by Axel Klenk • 920
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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 6 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 6 months ago by Axel Klenk • 920
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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 6 months ago by Axel Klenk • 920
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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 6 months ago by Axel Klenk • 920

Latest awards to Axel Klenk

Popular Question 3 months ago, created a question with more than 1,000 views. For Download problem with GEOquery::getGEO()
Scholar 7 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Limma un moderated t-test
Scholar 19 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Centurion 19 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 2.8 years ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 2.9 years ago, voted at least 25 times.
Teacher 4.0 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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