User: tenger929

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tenger9290
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Posts by tenger929

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Comment: C: [clusterprofiler] Transformation from ENSEMBL ID to entrez ID or Symbol got redu
... Thanks for your kindly reply. My RNAseq (mouse species) was obtained from strand specific RNA library,and we got gene list with Ensembl ID by DESeq2. In enrichment analysis by clusterprofiler developed by Prof. Yu.,Entrez ID is prefered. I have no idear why so large proportion of genes are unmapped ...
written 6 months ago by tenger9290
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[clusterprofiler] Transformation from ENSEMBL ID to entrez ID or Symbol got reduced number of genes
... Dear, It is convenient to use clusterprofiler in enrichment analysis. However, there is a problem confusing me in ID transformation. I have a gene list containing 39570 genes with ensembl ID. 1. After transformation with bitr function from Ensembl to entrez ID, the number of genes is 22142, 44.39% ...
clusterprofiler written 6 months ago by tenger9290 • updated 6 months ago by James W. MacDonald50k
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Comment: C: [DESeq2] Pre-filtering counts got different results after running results
... Hello, I have one more question. As prefiltering and non-prefiltering genes of zero counts in all samples will give different padj values, may I choose prefiltering or not, and which padj values I should take. Sincerely. ...
written 7 months ago by tenger9290
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Comment: C: [DESeq2] Pre-filtering counts got different results after running results
... Thank you very much! ...
written 7 months ago by tenger9290
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Comment: C: [DESeq2] Pre-filtering counts got different results after running results
... Thanks for your kindly reply. I am confused about how pre-filtering genes of zero counts in all samples got different results from non-prefiltering. For example, the padj values of ENSMUSG00000056290 were 0.049762917 and 0.050350481 in prefiltering and non-prefiltering,respectively. I only removed ...
written 7 months ago by tenger9290
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[DESeq2] Pre-filtering counts got different results after running results
... Hello,  After constructing DESeqDataSet, I firstly pre-filtered genes of zero counts in all samples , then running DEseq and results. However,  I found that padj values of some genes in pre-filtering condition were differnt from non-prefiltering. For example,                                        ...
deseq2 written 7 months ago by tenger9290 • updated 7 months ago by Michael Love23k

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