User: manoharankumar01

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Posts by manoharankumar01

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DEGs with High number of reads in one sample than the other
... Hi, Consider If one has two samples, sample A with 20 million reads and samples B with 40 million. When we compare these two sample read count and DGE using TMM normalizatoin method? The result will be biased towards sampleB? In other words can we compare two samples one having double the number ...
tmm normalised values written 2.7 years ago by manoharankumar010
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DESeq pvalue & padj
... Hi, How does pvalue and padj value in DESeq is calculated for samples With no replicates? gene baseMeanA baseMeanB foldChange log2FoldChange pval padj Adora2b 151.4009921842 1304.7338537888 8.6177364822 3.1073089836 0.0002 0.0602 Gs ...
deseq written 2.7 years ago by manoharankumar010 • updated 2.7 years ago by Gavin Kelly560
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edgeR bcvvalue related significant number of genes
... Hi, For few of my plant samples with no biological replicates I am using edgeR. If I use bcvvalue 0.1, I am getting >10k significantly differential expressed transcripts out of 47310 transcripts. If I use bcvvalue 0.4, I am getting ~5k significantly differential expressed transcripts out of 47 ...
edger written 2.7 years ago by manoharankumar010 • updated 2.7 years ago by Gordon Smyth38k
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Answer: A: TPM for miRNA tags
... Hi Lorena, Thanks for your reply, Do you want TPM for some specific reason? Yes, To find the novel miRNAs. I also had the same doubt but I saw this tpm value used in this publication (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-12-r145 : in Fig 1) for novel miRNA predicti ...
written 3.1 years ago by manoharankumar010
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TPM for miRNA tags
... Hi All, How one can calculate TPM (Transcripts per million) for miRNA tags/reads counts? eg:  miRNAids S_1.readcou S_2.readcou mmu-let-7a-1-3p    421    230 mmu-let-7a-5p    68708    26836 mmu-let-7b-3p    26    7   Thanks, Manoharan ...
mirna written 3.1 years ago by manoharankumar010
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Answer: A: normalized read count per group from edgeR
... Dear Aaron Lun, Thank you very much. Best Regards, Manoharan ...
written 3.6 years ago by manoharankumar010
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normalized read count per group from edgeR
... Dear All, I am using following code for my expression analysis from the edgeR package. data = read.table("mirna.readcout", header=T, row.names=1, com='') col_ordering = c(1,2,3,4,5,6) rnaseqMatrix = data[,col_ordering] rnaseqMatrix = round(rnaseqMatrix) rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqM ...
edger microrna written 3.6 years ago by manoharankumar010

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