User: Claire

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Claire0
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Posts by Claire

<prev • 23 results • page 2 of 3 • next >
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
... In the workflow of edgeR I found it used "keep <- rowSums(cpm(y)>0.5) >= 2". It said "As a rule of thumb, we require that a gene have a count of at least 10–15 in at least some libraries before it is considered to be expressed in the study." Its library size is a little smaller than mine. S ...
written 5 weeks ago by Claire0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... What I am going to measure is the gene's expression values (which I hope correspond to protein levels). ...
written 5 weeks ago by Claire0
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
... In my understanding, CDS is more meaningful, since differential expression at the CDS level indicates potentially different protein outputs...Is this acceptable? Does this behavior have big flaws? ...
written 5 weeks ago by Claire0
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Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
... I have a set of RNA seq data with replicates of 2 for each condition. The library sizes range from 16970950 to 36720407 (shown below). > DGEList$samples     group lib.size norm.factors A1     A   31271688            1 A2     A   36720407            1 B1     B   16970950            1 B2     B   2 ...
rnaseq edger written 5 weeks ago by Claire0
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When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
... When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?   ...
rnaseq edger deseq2 featurecounts written 5 weeks ago by Claire0 • updated 5 weeks ago by Gordon Smyth32k
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Comment: C: GO analysis under-represented genes and over-represented (enrichment) down-regul
... Yes, I know that. I want to know if it is necessary to do under-represented genes analysis... ...
written 5 weeks ago by Claire0
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GO analysis under-represented genes and over-represented (enrichment) down-regulated genes
... I did GO enrichment analysis on all of the DE genes, up-regulated genes and down-regulated genes separately. Since over-represented (enrichment) are easy to understand, I want to know what is the biological significance of under-represented genes? Can I say under-represented genes have similar bio ...
rnaseq go topgo clusterprofiler written 5 weeks ago by Claire0
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How many genes are appropriate for GO enrichment analysis
... Hi all, I got a list of differential expressed genes about 4000. I want to do the GO enrichment, can I use all the DE genes? What is the appropriate number of genes to do GO enrichment analysis? ...
go annotate clusterprofiler rna-seq written 5 weeks ago by Claire0 • updated 5 weeks ago by k.vitting.seerup10
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Comment: C: DIfferent mm10 gtf annotation files cause big difference in percentage of succes
... Sorry, there is a small difference in the parameters I din't notice before. When I change this parameter GTF.featureType="CDS" to GTF.featureType="exon", I got simmilar results... ...
written 6 weeks ago by Claire0
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