User: vedran.franke

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Germany
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3 months ago
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2 years, 10 months ago
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Posts by vedran.franke

<prev • 20 results • page 1 of 2 • next >
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Batch correction with uncertain biological variables
... I am currently trying to analyze a set of expression experiments from different tissues. Some of the expression profiles originate from knockout experiments, for which we expect to cause trans-differentiation. The experiments suffer from strong batch affects which are unknown, but fortunately, not ...
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biomaRt error in useMart
... When I run the following command: mart = useMart("ensembl", dataset="mmusculus_gene_ensembl") I get the following error: Error: 1: Entity 'copy' not defined I have never seen an error like this, and have no idea what might have caused it. Thank you in advance. ...
biomart written 7 months ago by vedran.franke0 • updated 7 months ago by Mike Smith2.1k
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DataFrame showAsCell function
... Quite often I use a DataFrame objects as columns in other DataFrame object. The inbuilt showAsCell generic does not natively support this - would it be possible to include such a function into one of the next releases of the s4vectors package? I use the following method:   setMethod("showAsCel ...
s4vectors written 13 months ago by vedran.franke0 • updated 13 months ago by Michael Lawrence9.8k
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ComplexHeatmap Legend labels
... When I specify  heatmap_legend_side = "bottom", legend_direction='horizontal' and nrow=1,   is it possible to put the legend labels below the color scale, and not to the right of each box? Best regards,    Vedran   ...
complexheatmap written 15 months ago by vedran.franke0
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Comment: C: normalizationFactors and library size
... Dear Michael,  Thank you so much for your prompt response. Everything is clear now. Best,  Vedran       ...
written 15 months ago by vedran.franke0
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normalizationFactors and library size
... I am a bit confused on how to use normalizationFactors in DESeq2. In the manual it says that "Normalization factors should include library size normalization". Does that mean that I should divide each column of the normalization matrix by the  corresponding sizeFactor, or it will be done automati ...
deseq2 written 15 months ago by vedran.franke0 • updated 15 months ago by Michael Love15k
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Comment: C: summarizeOverlaps on stranded paired end RNAseq data
... I have set ignore.strand=FALSE, single.end=FALSE, fragments=TRUE and in BamFileList, asMates=TRUE. The problem is that when I create 2 mock transcripts that have same coordinates and differ only in the strand, I  get almost the same number of reads for both transcripts, even though the fragments c ...
written 20 months ago by vedran.franke0
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summarizeOverlaps on stranded paired end RNAseq data
... Does summarizeOverlaps work with stranded paired-end RNAseq data? Will it assign fragments to the proper strand? Best regards,  Vedran     ...
summarizeoverlaps written 20 months ago by vedran.franke0
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Comment: C: IRanges start bigger than end
... The problem arose when a student used a combination of trim(shift()) on a GRanges object, and obtained a range with coordinates of start=1 and end=0. This makes sense now. Thank you so much!   ...
written 21 months ago by vedran.franke0
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Comment: C: IRanges start bigger than end
... Thank you for the prompt answer! I edited the question for the clarification - width was a typo. Could you please just clarify the logic behind this implementation? I still do not see why the above creates a valid IRanges object?   ...
written 21 months ago by vedran.franke0

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