User: heyao

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heyao30
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Posts by heyao

<prev • 9 results • page 1 of 1 • next >
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Comment: C: scRNA-seq : Classification of cell cycle phase
... Just curious about "simply perform Wilcoxon tests between each pair of phases using each individual cell's expression profille, Each cell is assigned to the phase where its genes have the highest expression. " How to do test within each individual cells ? Is that a simple and effective way to quant ...
written 21 days ago by heyao30
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Test genes expressed ( not just expressed higher ) in one or two group
... In terms of limma/edgeR usage, this seems to be a weird question. However, my question is for such situation: Assuming I collected lots of single cell datasets, and I have a set of candidate genes. What I want to ask/test is that: Is there some genes only expressed in some cell types ? I can build ...
limma edger written 6 weeks ago by heyao30 • updated 6 weeks ago by Gordon Smyth37k
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Comment: C: Is lmFit() the fastest way to fit thousands of linear model in R and use what a
... Thank you  James and Aaron, the answer and comments explain what I want to know clearly ! ...
written 6 months ago by heyao30
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Is lmFit() the fastest way to fit thousands of linear model in R and use what algorithm make it so fast ?
... Hi all, I just noticed that lmFit() is quite fast for linear model fit even for very big single cell data. This make me curious that how fast does lmFit() achieve but I haven't found any benchmarking results about that. If lmFit() is actually the fastest way for simple linear model fit,  I guess ...
limma written 6 months ago by heyao30 • updated 6 months ago by James W. MacDonald50k
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Answer: A: How can I compare the expression of two genes within the same sample?
... You can transform your raw counts to FPKM or TPM (recommend) for such within-sample comparsion, as these two normalization both takes gene length into consideration. ...
written 6 months ago by heyao30
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How to quantify or decide whether a covariate should be included in the linear model for differential expression analysis ?
... Hi everybody, I am not sure if I asked a totally stupid or unnecessary question here, but this is an actual question bothering me for a long time after I learned how to perform differential expression analysis using tools like limma/edgeR/DESeq recently. We all know that the mainstream DE analysis ...
limma edger deseq2 written 6 months ago by heyao30 • updated 6 months ago by James W. MacDonald50k
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Comment: C: scran: Are the log counts expression comparable among different genes within a s
... Thanks a lot ! Sometimes I  also see people trying to define whether a gene is expressed in a cell using TPM > 1 (read-based ) or UMI counts > 1 as cutoff. A typical case is to define whether a T cell is CD4+ or CD8+ T cell. Since the gene capture difference is quite different, I am not sure i ...
written 6 months ago by heyao30
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Comment: C: scran: Are the log counts expression comparable among different genes within a s
... Thanks for your quick reply and detailed response. I guess there is some misundering here since my question is more about visualisation but not about scientific question. Several single cell paper would like to show markers gene expression for each cluster like that:  Highly Parallel Genome-wide Ex ...
written 6 months ago by heyao30
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scran: Are the log counts expression comparable among different genes within a sample/cell ?
... In my understanding, applying size factor to raw count by scater::normalize() is one type of between-sample normalization. Thus the expression within the same gene are comparable among different sample/cells. However, the size factor seems to doesn't account for gene length effect like TPM, so it sh ...
scran scater written 6 months ago by heyao30 • updated 6 months ago by Aaron Lun24k

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