User: naktang1

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naktang10
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Posts by naktang1

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The number of the counts columns uploaded to the Deseq2 affected the number of reported DEG
... I has just started using Deseq2 to discovery deferentially expressed genes (DEGs). In my data, I have 6 strains (S2,S3,S4,S5,S6,S7), each of which was studied at 2 time points (T1,T2), under 2 conditions ( drought, water), and with 2 replicates. I performed the analysis like this: 1) Upload count ...
deseq2 written 3 months ago by naktang10
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Comment: A: very low number in normalized count but give very high in log2foldchange
... thank you for you reply, However what threshold level for LFC that you will recommend to use lfcshrink function ...
written 13 months ago by naktang10
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very low number in normalized count but give very high in log2foldchange
... I have one gene that have very high in log2foldchange. gene baseMean log2FoldChange lfcSE stat pvalue padj geneA  50.46458 41.13637 3.733037 11.01955 ...
deseq2 written 13 months ago by naktang10
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Comment: C: find gene only express in one condition in Deseq2
... Thank you for your answer. Do you have some advice if I want to do this analysis like another package or another software ...
written 14 months ago by naktang10
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find gene only express in one condition in Deseq2
... If I want to identify gene which express in one condition. Is it possible in deseq2. Because I think Deseq2 calculate logfoldchange for the gene that express in two condition  and test statistic for significant gene. However it will produce the gene that express in higher or lower but not the gene t ...
deseq2 written 14 months ago by naktang10 • updated 14 months ago by Michael Love22k
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how to select a result output from multiple factor design in deseq2
... I also read in vignette and many post about multiple factor design but I still don't get it.What I want is to compare between the same cell type and also in the same day but different in heat condition. For example Day0cellABCheatC VS Day0cellABCheatH So I design a condition as follow which I'm no ...
deseq2 written 19 months ago by naktang10 • updated 19 months ago by Michael Love22k
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Biostrings: problem to access indel-details (nucleotide sequence) form pairwiseAlignment()
... How to get the nucleotide at the indel position after I use pairwise pairwiseAlignment() It is easy way to get the position of indel  of pattern or subject in pairwiseAlignment() For example, start(indel(pattern(align)))) ## can get indel position in pattern start(indel(subject(align)))) ## c ...
biostrings bioconductor written 3.6 years ago by naktang10 • updated 3.6 years ago by Hervé Pagès ♦♦ 13k

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