User: jomo018

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jomo018540
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Posts by jomo018

<prev • 87 results • page 1 of 9 • next >
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... Yes, I realize that. However, if **p-value** is insignificant, I am not sure whether my estimate for that gene is correct. So I prefer discarding that gene altogether rather than placing it incorrectly in the ranked list. ...
written 8 weeks ago by jomo018540
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Answer: A: GSEA PreRanked lists from DESeq2 results table
... I tend to view p-values and adjusted p-values as a confidence measures, not enrichment measures, therefore less fit for GSEA. Results for genes with high (bad) p-value are simply not reliable and should not be used for further analysis. Once you determine a p-value threshold, I would argue that FC ...
written 8 weeks ago by jomo018540
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Answer: C: RRBS analysis using methylkit with 2 variables
... I haven't actually tried your exact workflow however I believe you can use `reorganize` to select samples for downstream. The command should be inserted in your case between `unite` and `calculateDiffMeth`. ...
written 4 months ago by jomo018540
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Answer: C: Maths implications: log2 transformation before or after normalisation
... Log2 is monotonic but a non-linear transformation. The ratios between elements in a sample are not kept. Once performed, a downstream **linear** operation such as depth normalization is less appropriate. In such cases, it makes more sense to begin with the linear operations and end with non-linear o ...
written 5 months ago by jomo018540
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Comment: C: RNAseq differential expression analysis : no significative FDR but significative
... I have encountered this situation quite a few times and tend to accept and report results based on GO/Pathway enrichment significance. One argument is that DE p-value < 0.05 and fdr > 0.05 does not mean your full set of genes is insignificant. Rather, your set of genes is likely to **include** ...
written 5 months ago by jomo018540
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Comment: C: DESeq2: (1) Comparing multiple groups using a for loop & (2) normalization of ti
... Change caseA definition to `caseA <- as.character(samplelist[1])` and add a comma after `file = paste("output", caseB, "vs", caseA, ".tsv")`. ...
written 5 months ago by jomo018540
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Comment: C: subsetting matrix elements and creating a histogram
... Data point 5625 is dominating the histogram cell size. You can zoom in for example with `hist(x,breaks=1000,xlim=c(0,400))` or just exclude outlier/s. The issue here is R and plot related. You should explore the reason for the outlier though. ...
written 5 months ago by jomo018540
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Comment: C: subsetting matrix elements and creating a histogram
... The data point in this case is characterized by a name and by a value. You don't need to separate value from name. You can create a name-less vector for example with `y=as.numeric(x)` but it's not required. What does `summary(x)` show? ...
written 5 months ago by jomo018540
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Comment: C: RRBS Methylation integration with RNA-seq differential expression
... Methylated promoter inhibits expression. If you examine just one individual CpG, rather than average across the promoter, how can you deduce its functionality? ...
written 8 months ago by jomo018540
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Comment: C: FASTQ alignment result is really bad
... Just to put aside anything related with SRA, you can directly download fastq files for your project here: https://www.ebi.ac.uk/ena/data/view/PRJNA389279][1] I have looked at one file and indeed it looks like color-space: @SRR5644749.11183773 11183773/2 T220330222222312020021131122222210 ...
written 16 months ago by jomo018540

Latest awards to jomo018

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Pair end merging and statistical output
Scholar 4 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Popular Question 5 months ago, created a question with more than 1,000 views. For Pair end merging and statistical output
Popular Question 8 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Popular Question 11 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Popular Question 14 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

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