User: sina.nassiri

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sina.nassiri50
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Switzerland/Lausanne
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Posts by sina.nassiri

<prev • 14 results • page 1 of 2 • next >
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Comment: C: tximport - using hg38 with RefSeq (NM) and Gene Symbol
... Thanks for the prompt reply, Mike. I am facing the same error as Sebastian, and I fully understand the logic behind removing duplicate rows in the provided example. However, in my case (and perhaps also in Sebastian's), the scenario does not include presence of duplicate rows, but rather mapping of ...
written 8 months ago by sina.nassiri50
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Comment: C: tximport - using hg38 with RefSeq (NM) and Gene Symbol
... Dear Mike, when dealing with 1-to-many mappings in tx2gene table as in Sebastian's case, shouldn't the first occurrence of the tx in question also be removed? In your suggested workaround, the first tx id is kept and the rest are tossed. Could you please elaborate on the logic behind this workaround ...
written 8 months ago by sina.nassiri50
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Comment: C: Single Sample GSEA (ssGSEA) and dynamic range of expression
... Sorry for the super late reply. My question was directly about the ssGSEA algorithm of Barbie et al. The first normalization that you're referring to, is the normalization prior to ranking via ecdf as proposed by Hänzelmann et al and implemented in the GSVA package. This normalization does address m ...
written 9 months ago by sina.nassiri50
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
... I completely agree with you on using full model + SVs, but in this case neither one of "sex","age", and "city" is a variable of interest. Am I missing something here? ...
written 13 months ago by sina.nassiri50
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
... 1) I'd go with the former, because in the latter you're throwing out potentially valuable information about study design. 2) Sure; I missed cell type composition. 3) You are right about svaseq being similar to using sva with v$E; I just double checked the source code. My bad! ...
written 14 months ago by sina.nassiri50
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Answer: A: Extracting subclusters from original data
... I'm not familiar with ComplexHeatmap, but if it produces a tree (as resulting from hclust e.g.) you can directly pass it to cutree(). ...
written 14 months ago by sina.nassiri50
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Answer: A: Applying sva is compatible with limma duplicateCorrelation?
... In principle, if you don't include 'patient' in the full model (mod) it will be captured by SVA (assuming that it has a significant contribution to the overall variation observed). However, there are a few points to consider: 1- You have already included sex, age, and city in the null model during ...
written 14 months ago by sina.nassiri50
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Single Sample GSEA (ssGSEA) and dynamic range of expression
... Dear ssGSEA users, In ssGSEA, gene expression values for a given sample are rank-normalized, and an enrichment score is produced using the Empirical Cumulative Distribution Functions (ECDF) of the genes in the signature and the remaining genes [Barbie et al., 2009]. The part that I'm having a hard ...
gsva piano ssgsea egsea written 14 months ago by sina.nassiri50
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Answer: A: DESeq2 DESeqDataSetFromTximport design formula
... Not sure what you mean by "paste together whichever factors I want to compare further down the line", but the problem with matrix not being full rank is that the columns for condition and eya1six1 are linearly dependent in the design matrix, i.e. condition and eya1six1 are confounding. What's your e ...
written 16 months ago by sina.nassiri50
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Comment: C: GSVA indifferent to 'abs.ranking'
... Dear Dr. Castelo, Thank you for the feedback. I upgraded to the latest version (1.24.1) and reran the example above. Results from abs.ranking=TRUE and abs.ranking=FALSE are no longer identical, but I'm still confused about the utility of abs.ranking. Let's return to above example in which set4 is a ...
written 16 months ago by sina.nassiri50

Latest awards to sina.nassiri

Popular Question 15 months ago, created a question with more than 1,000 views. For Single Sample GSEA (ssGSEA) and dynamic range of expression
Supporter 15 months ago, voted at least 25 times.
Student 15 months ago, asked a question with at least 3 up-votes. For GSVA indifferent to 'abs.ranking'
Scholar 16 months ago, created an answer that has been accepted. For A: SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)

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