User: hffqyd

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hffqyd10
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Posts by hffqyd

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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... 1. I supposed the treat2 looked to have been used in the "contrast"; 2. I had already posted to [https://support.bioconductor.org][1], thanks; 3. Below is the output of resultsNames(dds): > > resultsNames(dds) > > [1] "Intercept" > > [2] "group_treat1_vs ...
written 8 weeks ago by hffqyd10
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Sorry for replying late. I updated the DESeq2 normalized counts above. Thanks for your reply. ...
written 9 weeks ago by hffqyd10
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Sorry for replying late. 1. I updated the DESeq2 normalized counts; 2. Yeah, gene7 is fine, I pasted the wrong line; 3. If I didn't count wrong, there about 2% genes seemed non-intuitive like this. 4. I merged the original counts data to the result by gene symbol; Thanks for your reply. ...
written 9 weeks ago by hffqyd10
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... gene5, gene6, gene7, gene8. ...
written 9 weeks ago by hffqyd10
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Thanks for your reply. Yes, the lines in the head of result did indicate the logFC corresponding to treat1/control of group. But, as mentioned above, some of the logFC looked odd. > head(result) log2 fold change (MLE): group treat1 vs control Wald test p-value: group treat1 vs con ...
written 9 weeks ago by hffqyd10
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Thanks for your reply, I checked but I didn't mix up. ...
written 9 weeks ago by hffqyd10
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Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Hi, I'm new to RNA-seq and differentially expressed gene (DEG) analysis using DESeq2, the R package. But I encountered a problem need for help. The experiment has samples of 3 group (control, treat1, treat2) with 3 replications each. Having RNA-sequenced, the reads counts were inputed to DESeq2 fo ...
deseq2 differentially expressed genes rna-seq written 9 weeks ago by hffqyd10

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