User: 15958021290

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Posts by 15958021290

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Comment: C: DESeq2 VS edgeR DEG results different in analysis same data
... Thank you for your suggestion again! And I have tried other two datasets,I find these two datasets results are identical in using DESeq2 and edgeR. So I think may be there is some wrong with my first dataset or it's a very mysterious dataset. I will remember your kindly advice! ...
written 9 days ago by 159580212900
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Comment: C: DESeq2 VS edgeR DEG results different in analysis same data
... Thank your for suggestion! I have edit my question! And I know your No.1 point. What I want to say is "without filter raw deg result based on |logFC| and padj/FDR. Not "without filter count" .I know both edgeR and DESeq2 would filter low count in the process. ...
written 9 days ago by 159580212900
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DESeq2 VS edgeR DEG results different in analysis same data
... Hi. I have a problem about different DEG result from analysis same data using DESeq2 and edgeR. Here is two raw all DEG result without fiter based on |logFC| and padj/FDR ``` # DESeq2 23000 gene baseMean log2FoldChange lfcSE stat pvalue padj AT1G61780 849.0853127 -8.903695371 0.466024423 -19.10564 ...
edger deseq2 written 9 days ago by 159580212900 • updated 9 days ago by Gordon Smyth38k
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Comment: C: Does edgeR need to specify reference group?
... Thank you! It helps! Your answer are accepted! ...
written 13 days ago by 159580212900
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Comment: C: Does edgeR need to specify reference group?
... Thank you! Your detailed answer are very helpful to me! Sorry for no patient to carefully read the manual! ...
written 13 days ago by 159580212900
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Does edgeR need to specify reference group?
... Hi guys! I want to know if edgeR also need to specify reference group data similar to DESeq2? Because DESeq2 need to use ``` dds$condition <- factor(dds$condition, levels = c("untreated","treated")) # or dds$condition <- relevel(dds$condition, ref = "untreated") ``` to specify which group is r ...
edger reference group written 13 days ago by 159580212900 • updated 13 days ago by Gordon Smyth38k
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Comment: C: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Thank you for your kindly advices. Sorry to bother you. ...
written 9 weeks ago by 159580212900
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Comment: C: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Thank you for your reply! And what do you think of equalLibSize() fucntion using to output so called "normalized count" like this example https://stats.stackexchange.com/questions/165056/tmm-normalization-of-rna-seq-data-in-r-language-using-edger-package ...
written 9 weeks ago by 159580212900
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the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... Hi guys, I want to talk about the the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR.And I want get advice from you about my opinion below: firstly, two methods is similar, they calculate respective scale factor at first.And then they should divided by scale factor to nor ...
normalization edger deseq2 written 9 weeks ago by 159580212900 • updated 9 weeks ago by Gordon Smyth38k
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Comment: C: how to get normalized count data from edgeR using TMM methods
... Thank you for your comment! Actually I want to talk about the two normalization(MRN and TMM) methods supplied by DESeq2 and edgeR. two methods is similar, they calculate respective scale factor at first.And then they should divided by scale factor, and DESeq2 prodvide counts(dds, normalized=T) to d ...
written 9 weeks ago by 159580212900

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