User: Benjamin Ostendorf

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United States
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bnostendorf
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1 year, 1 month ago
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Posts by Benjamin Ostendorf

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Error in TCGAquery of TCGAbiolinks Package
... Hi Beginner, after the transfer of the TCGA data to GDC the commands changed - try GDCquery instead of TCGAquery. Also make sure you have the latest version of TCGAbiolinks installed and take a look at the current vignette.  Best, Benjamin ...
written 13 months ago by Benjamin Ostendorf80
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Comment: C: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Hi Konstantinos,  regarding 1: In my view it is totally worth to apply DESeq2 - it's just a couple of lines of code and there's less room to make mistakes than doing the statistics yourself. If you really want to you can also switch off independent filtering in the results function (independentFilt ...
written 13 months ago by Benjamin Ostendorf80
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Answer: A: Comparing means of VST tranformed RNA-Seq counts in different groups of samples
... Hi Konstantinos,  in order to assess differential expression of genes I would use DESeq2's built-in function DESeq. It takes as input a DESeqDataset object, which is similar to a summarized experiment; it's all described well in the vignette. DESeq internally normalizes the samples (to library size ...
written 13 months ago by Benjamin Ostendorf80
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Comment: C: Log2FoldChange shrinkage method in DESeq2
... Thanks Michael, I'll read up on and try out the s-values! ...
written 13 months ago by Benjamin Ostendorf80
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Comment: C: Log2FoldChange shrinkage method in DESeq2
... Thanks for your reply, Michael! I'm comparing 8 versus 5 biological replicates; the data were generated using Lexogen's 3' Quantseq kit, which generates just one fragment per transcript close to the 3' end. Please find below the MA-plot using ashr-shrunken LFCs. lfcShrink with ashr gave this warni ...
written 13 months ago by Benjamin Ostendorf80
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Log2FoldChange shrinkage method in DESeq2
... Hi everyone,  I noticed that applying the newly recommended apeglm method for logfoldchange-shrinkage when using the DESeq2 package resulted in a very different MA-plot in comparison to setting the lfcShrink method to normal ; it seems to shrink the logfoldchanges a lot more for most genes, possibl ...
deseq2 lfcshrink apeglm written 13 months ago by Benjamin Ostendorf80 • updated 13 months ago by Michael Love24k
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Comment: C: Retrieve accurate tumor stage data with TCGAbiolinks
... Thanks for your pointers, Marcel -  I'll check these and compare them!  ...
written 13 months ago by Benjamin Ostendorf80
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Retrieve accurate tumor stage data with TCGAbiolinks
... Hi everyone,  I'm wondering how to retrieve the most accurate tumor stage at diagnosis information for the TCGA-SKCM dataset using TCGAbiolinks. I need stage information only in format stage I-IV.  I retrieved the variable 'tumor_stage' as part of the indexed clinical data (using ‚GDCquery_clinic‘ ...
tcga tcgabiolinks written 13 months ago by Benjamin Ostendorf80

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