User: Anja Rockstroh

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6 years, 10 months ago
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Posts by Anja Rockstroh

<prev • 6 results • page 1 of 1 • next >
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Comment: C: GSVA on RNAseq data
... Thank you for the very helpful comments! ...
written 5 weeks ago by Anja Rockstroh20
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Comment: C: GSVA on RNAseq data
... Thanks for the reply and apologies for the wrong assumption that 'counts' was the recommended input unit for RNAseq data - it was based on the fact that 'counts' were used for all RNAseq examples in the package vignette and the original publication. However, the 'counts' used in those examples have ...
written 5 weeks ago by Anja Rockstroh20
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GSVA on RNAseq data
... For GSVA scoring on RNAseq data, the authors recommend to use 'counts' as input data (with kcdf="Poisson"), but also briefly mention the options to use logCPM, logTPM or logRPKM (with kcdf="Gaussian") as input. Since the first step in the GSVA scoring algorithm is to rank the genes by their expressi ...
rnaseq gsva written 6 weeks ago by Anja Rockstroh20 • updated 6 weeks ago by Robert Castelo2.3k
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Comment: C: Differential expression on GSVA scores using LIMMA
... Thank you - that confirms my thoughts on the topic. However, even though we can't really express the difference between two GSVA scores in terms of a 'traditional' fold-change, one may still like to use some measure that describes the extend/magnitude of change between two scores (e.g. the differenc ...
written 6 weeks ago by Anja Rockstroh20
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Differential expression on GSVA scores using LIMMA
... I am using limma on GSVA scores to assess differential expression of gene sets (in microarray and RNAseq data). Since GSVA scores can be negative, I am wondering how limma calculates the fold changes between a negative and a positive GSVA score and how meaningful a fold change cutoff would be to def ...
limma gsva written 7 weeks ago by Anja Rockstroh20 • updated 7 weeks ago by Robert Castelo2.3k
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overview function of made4
... Hello Aedin, I noticed that the default colours the overview function of the made4 package is using is the 21 colour palette of getcol. However, I was wondering whether this can be changed to custom colours? I have tried to include arraycol or cols into the overview function, but I always get the " ...
cancer prostate written 6.9 years ago by Anja Rockstroh20 • updated 6.9 years ago by Martin Morgan ♦♦ 23k

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