User: sup230

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sup23010
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Posts by sup230

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Can't find gene list for KEGG genesets
... Thank you- This worked! Could you also help me with matching the KEGG gene IDs to either gene symbols, Entrez ID, or Ensembl IDs? ...
written 5 days ago by sup23010
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Can't find gene list for KEGG genesets
... Hi, I used both gage package in R and GSEA software for KEGG pathway analysis and since the 2 tools have different algorithms, I got slightly different results in the list of genesets. I was able to find the genes in each gene set from GSEA from their website, but I don't seem to find the gene list ...
kegg geneset gage package genelist written 5 days ago by sup23010 • updated 5 days ago by Gordon Smyth31k
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Comment: C: log2 fold change calculation for DE gene analysis
... Yes! This sounds like a much more efficient and right way. I have a couple followup questions though.  When I calculate the mean and standard deviation for the control group, I would only include the genes in a particular gene set, because higher z-score would still mean that gene set is more enric ...
written 10 days ago by sup23010
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log2 fold change calculation for DE gene analysis
... Hi,  I have questions that are not a part of typical RNAseq work flow so I would like lots of your input/help! I used DESeq2 to get the full list of DEgenes with their respective log2fc between the two phenotype groups in my data. The metadata are TCGA-LGG samples and I am interested in phenotype ...
deseq2 log2fc l2fc written 12 days ago by sup23010 • updated 11 days ago by Michael Love13k
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DESeq2 - GAGE workflow
... I have some confusion about GAGE workflow. I understand GAGE is a type of functional class scoring tools with no preset cutoff used to identify significant genes. But I have seen several workflow/model scripts where they used the output from DESeq2 which is selected based on p-adjusted value of 0.05 ...
deseq2 gage package written 19 days ago by sup23010
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Comment: C: DESeq function taking too long
... Can you elaborate briefly how different the two methods are between DESeq and limma-voom?  ...
written 27 days ago by sup23010
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Comment: C: DESeq function taking too long
... Thanks for the clarification!  The resource monitor shows 79% used physical memory: 6393 MB in use and 1653 MB available. The number of hard faults as listed under processes is 0 but on the graph to the right side, I see some peaks come and go. Any suggestion of soluiton if this seems to be the cau ...
written 27 days ago by sup23010
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Comment: C: DESeq function taking too long
... I am using Windows 10 Pro (v. 1703) 64 bit OS. I got this desktop about a month ago.  It says that the installed RAM is 8GB and 7.89 GB is usable. I am not completely sure what you meant by swapping to disk..? ...
written 27 days ago by sup23010
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Comment: C: DESeq function taking too long
... Can you clarify how to remove genes with very small counts? Should I look at normalized counts (not the rawcounts?) and remove the genes with normalized counts less than 10 in most samples?  I have tried with 100 samples for all 56730 genes and it took about 15 min to do DESeq. Also, when I tried a ...
written 28 days ago by sup23010
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DESeq function taking too long
... Hi,  I am running DESeq function in DEseq2 (version 1.16.1) and it's taking too long . I had it running over night and it's still not done.  I am thinking it's because my data are too big because I was able to run it with smaller dataset. My countdata is made of 56730 genes from 475 samples and I ...
rnaseq deseq deseq2 factor written 28 days ago by sup23010 • updated 27 days ago by Peter Langfelder1.3k

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