User: melkile26

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melkile260
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Posts by melkile26

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Comment: C: How to find Top 10 expressed genes in DESeq2
... Is this because baseMean doesn't take into account the differences in library sizes between samples ...
written 8 months ago by melkile260
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Comment: C: How to find Top 10 expressed genes in DESeq2
... Dear Michael, Thanks for your replay, Are you recommending to extract the top expressed genes based on adjusted p-value rather than sorting baseMean? Best regards, Mel ...
written 8 months ago by melkile260
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How to find Top 10 expressed genes in DESeq2
... I am a newbie to RNAseq analysis. Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. I removed rows that have no counts, or only a single count across all samples using the cod ...
deseq2 differential gene expression rnaseqgene basemean written 8 months ago by melkile260 • updated 8 months ago by swbarnes2330
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Comment: C: how to find expressed genes in RNAseq
... Dear Michale, As I mentioned, I found the gene level counts using featureCounts, can I use tximport to import the gene level count matrix which I found using featurCounts. After importing, I am thinking to use TPM to find the expressed genes.   ...
written 9 months ago by melkile260
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Comment: C: how to find expressed genes in RNAseq
... Hi Michael, Thanks for your reply, I just learned, even in using the command below doesn't related to in filtering the expressed genes, dds<-dds[rowSums(counts(dds)) > 5,] According to DESeq2 vignette, "removing rows in which there are no reads or nearly no reads, we reduce the memory size ...
written 9 months ago by melkile260
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how to find expressed genes in RNAseq
... Hello all, I am a newbie to RNAseq analysis. I am comparing (treatment vs control). Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. Before I start the deferentially expres ...
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GAGE for non model organism
... Dear All, I have a non model reference genome which is not found in in public databases, as it is mentioned in GAGE vingnatte, I used the following commands to generate the KEGG gene set kg.ko=kegg.gsets("ko") kegg.gs=kg.ko$kg.sets[kg.ko$sigmet.idx] and found the following results, $`ko00970 Am ...
gage gage package written 14 months ago by melkile260

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