User: Axel Klenk

gravatar for Axel Klenk
Axel Klenk • 920
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920
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Switzerland
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11 hours ago
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10 years, 4 months ago
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a*********@idorsia.com

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 7 months 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 10 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 10 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 10 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 10 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 10 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 10 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 10 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 10 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 10 months ago by Axel Klenk • 920

Latest awards to Axel Klenk

Popular Question 7 months ago, created a question with more than 1,000 views. For Download problem with GEOquery::getGEO()
Scholar 11 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Limma un moderated t-test
Scholar 23 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Centurion 23 months ago, created 100 posts.
Scholar 23 months ago, created an answer that has been accepted. For A: Limma un moderated t-test
Scholar 3.1 years ago, created an answer that has been accepted. For A: Limma un moderated t-test
Supporter 3.2 years ago, voted at least 25 times.
Teacher 4.3 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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