User: sunnykevin97

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sunnykevin97140
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Posts by sunnykevin97

<prev • 134 results • page 1 of 14 • next >
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What are the reasons to find so few Differentially expressed genes (DEGs)?
... HI, After the differential gene expression analysis, I had got only 15 genes with logFC < 1.5. Is it because of the Transcriptome reference annotation, expression quantification method, and DEG detection methods which are affecting the optimal filtering threshold ? Comments. ...
rna-seq written 5 weeks ago by sunnykevin97140 • updated 5 weeks ago by Antonio R. Franco4.6k
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Comment: C: R: How to convert log2FC (Fold Change) obtained by limma's topTable() function t
... Using the above function I converted logFC to normal FC values for three groups(MC,SC,OC). I'd like to compare the normal FC values among these groups, how do I say this particular gene has expressed more in this particular group ? Logfc = 0.58 2^(0.58) = 1.5 Foldchange I got very few diff ...
written 4 months ago by sunnykevin97140
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Comment: C: Which pipeline is the best for differentinal gene expression analysis (edgeR, DE
... I don't have alternate assembly, the non-model organism I'm working. ...
written 4 months ago by sunnykevin97140
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Comment: C: Which pipeline is the best for differentinal gene expression analysis (edgeR, DE
... Thanks,I'm working with non-model organism, only primary genome assembly (26 replicons) available currently. I'm interested only in the differential gene expression analysis. I started with TRINITY,HISAT2,featurecounts,edgeR,GO,KEGG. ...
written 4 months ago by sunnykevin97140
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Which pipeline is the best for differentinal gene expression analysis (edgeR, DESEQ2 or HISAT2 - stringtie - ballgown)?
... HI, I may asking a naive question, to clarify myself. Which RNA_seq pipeline considered to be the best for model and non-model organisms ? I used edgeR earlier, find it very easy. Can some one explain, which pipeline is the best edgeR, DESEQ2 or HISAT2 - StringTie - Ballgown How to select these too ...
rna-seq written 4 months ago by sunnykevin97140 • updated 4 months ago by Manuel Mendoza10
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Is their any tool tell us about housekeeping genes ?
... Hi After differential gene expression analysis I got around 300 genes, among these I'm interested to know how many of them are house keeping genes. Is their any tool based on the geneID it can tell us this is a house keeping gene or not ? Suggestions Thanks ...
rna-seq written 4 months ago by sunnykevin97140
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Comment: C: How to add images to a Biostars post
... Some situations this method not working. HTML method working best. ...
written 4 months ago by sunnykevin97140
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PCA using ggplot2/ggfortify autoplot function ?
... HI With the normalized+ transformed gene-counts information using autoplot function plotted the PCA. I had additional data something like hormonal levels(6 variables), is it possible to show that information as well along with the genecounts information on one PCA plot? autoplot(sample_pca, ...
rna-seq written 4 months ago by sunnykevin97140
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(Closed) PCA using autoplot function
... HI With the normalized+ transformed genecounts information using autoplot function plotted the PCA. I had additional data something like hormonal levels, is it possible to show that information as well along with the genecounts information in one PCA ? totally confused, some suggestions. ![PCA][1 ...
rna-seq written 4 months ago by sunnykevin97140
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Comment: C: Resources for gene signature creation
... That's ok, cortisol Actual values - c(42.14125,44.50375,50.21187,34.32312,26.25250,34.32312,31.96063) dff$cortisol.pred Predicted values - 47.5 42.7 45.1 36.3 29.1 31.5 31.5 ...
written 4 months ago by sunnykevin97140

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