User: psm

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psm30
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Posts by psm

<prev • 15 results • page 1 of 2 • next >
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GSVA kernels: Gaussian or Poisson?
... Hi all, this question has indirectly come up several times. What is the best kcdf setting to use for GSVA analysis on non-log or non-variance normalized TPM data? For GSVA analysis using RNAseq data, the GSVA manual states: "We calculate now GSVA enrichment scores for these gene sets using first ...
rna-seq written 3 days ago by psm30 • updated 2 days ago by Kevin Blighe61k
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Is the ssGSEA enrichment score affected by other samples in the analysis group?
... Hi all, I have an RNAseq data for 81 samples. I ran ssGSEA 2.0 (I cloned it from the Broad Institute's github repository and sourced the code through R). After running the analysis a first time, I was curious whether somehow the score generated for any given sample was affected by other samples pres ...
ssgsea R rna-seq written 15 days ago by psm30 • updated 9 days ago by lixuenan20080630
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Answer: A: Enrichment score of ssGSEA
... I'm not sure about the range but I have definitely obtained negative scores. I suppose it depends on the distribution of expression values for genes in the geneset vs distribution of expression values for all genes of that sample (my interpretation of the methods in their original paper) "The gene ...
written 15 days ago by psm30
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Comment: A: single cell sequencing data doublets removal tools selection
... I'm also interested in this question 1 year later... Anyone have any experience with any of these tools or assessed how well they perform? Thanks in advance. ...
written 4 weeks ago by psm30
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Comment: C: hisat2-build indexing produces more than 8 output files
... I know this post is old but just thought I'd reply to this specific comment since I struggled with this issue for a while - I think HISAT2 is supposed to produce exactly 8 files, and as Satyajeet Khare mentioned may be the most correct explanation. I also got more than 8 files every time my process ...
written 21 months ago by psm30
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Comment: C: ENSEMBL annotation file for quantification: which file to use?
... Thanks for breaking it down for me - that's exactly what I wanted to know. ...
written 21 months ago by psm30
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Comment: C: ENSEMBL annotation file for quantification: which file to use?
... Very helpful! Thanks for clarifying the different formats. ...
written 21 months ago by psm30
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Comment: C: ENSEMBL annotation file for quantification: which file to use?
... Thank you for that pointer - noted. Thankfully, if I understand correctly, Devon Ryan has pointed out that FeatureCounts is not impaired by this for UCSC and Ensembl chromosome names. ...
written 21 months ago by psm30
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ENSEMBL annotation file for quantification: which file to use?
... Hello, question regarding gene quantification for RNAseq: I've used HISAT2 to align my reads against the hg38 genome, and used UCSC annotation for this. I now want to perform gene-level quantification using featureCounts. On the Ensembl website (ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens ...
ensembl rna-seq annotation written 21 months ago by psm30 • updated 21 months ago by Ben_Ensembl1.5k
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Comment: C: hisat2-build indexing produces more than 8 output files
... I am having a similar issue - many .rf files but less than 8 .ht2 files. Was this ever resolved? Are they okay to use? ...
written 21 months ago by psm30

Latest awards to psm

Popular Question 20 months ago, created a question with more than 1,000 views. For RNA-seq: How to know which paired reads come from the same original fragment?
Popular Question 20 months ago, created a question with more than 1,000 views. For ENSEMBL annotation file for quantification: which file to use?
Popular Question 20 months ago, created a question with more than 1,000 views. For HISAT2: Extracting splice sites and exons for index

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