User: aishu.jp

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aishu.jp10
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Posts by aishu.jp

<prev • 9 results • page 1 of 1 • next >
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Comment: C: DESeq2 compare all_vs_all levels error
... But is it necessary to use lfcshrink in all_vs_all design comparison. Will it affect in identification of significant genes? What affect lfcshrink () will have in the expression values of genes? ...
written 3 months ago by aishu.jp10
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Comment: C: DESeq2 compare all_vs_all levels error
... Thank you so much. It was typo trouble After getting all the three combinations `day73 <- lfcShrink(dds, contrast=c("condition", "day7", "day3")) day71 <- lfcShrink(dds, contrast=c("condition", "day7", "day1")) day31 <- lfcShrink(dds, contrast=c("condition", "day3", "day1"))` In the re ...
written 3 months ago by aishu.jp10
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DESeq2 compare all_vs_all levels error
... I am currently working in plant pathogen interaction and is trying to make a gene co-expression network using RNA-seq data. I used HTseq-count to get the read counts. My dataset consist of Resis_treated (1st day, 3rd day and 7th day) samples taken under 3 time point with 2 replicated for each time ...
rnaseq deseq2 error written 3 months ago by aishu.jp10 • updated 3 months ago by swbarnes2330
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DESeq2: thousands of NA for pvalues?
... I have a RNA seq data which I am trying to identify DEGs. Dataset contains three sets of Untreated - 2 replicates and Treated - 2 replicates. My DEseq2 results shows padj values NA and some p values and padj values as zero. A total of 3000 genes shows such result. I tried using **res <- results ...
deseq2 rna-seq degs cooks cutoff written 9 months ago by aishu.jp10 • updated 9 months ago by Michael Love25k
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How to manage self loop in gene coexpression network constructed using Pearson correlation in Cor() function
... Hai, I have a control vs treated RNA-seq plant data for which I am trying to construct gene coexpression network.I identifed a total of 6000 genes are significantly differential expressed genes using DESeq2 R package after applying FDR cutoff 0.05. The normalised count matrix of these 6000 genes de ...
rna-seq desq2 pearsoncorrelation gcn written 16 months ago by aishu.jp10
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Comment: C: DESeq LRT test and construction of Co-expression network
... Thank you for helping me ...
written 19 months ago by aishu.jp10
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DESeq LRT test and construction of Co-expression network
... I have a RNA seq data which I am trying to identify DEGs. Dataset contains Untreated - 2 replicates (time point 0hr) Treated - 4 replicates (2 replicates at 6hr and 2 replicates at 12 hr) I merged all the samples and tried to identify DEGs untreated vs treated as well as I compared the samples using ...
deseq2 network analysis lrt co-expression network time course experiment written 19 months ago by aishu.jp10 • updated 19 months ago by Peter Langfelder2.2k
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Comment: C: DEseq2 sample imbalance
... After doing the LRT test, to identify the significant genes the cutoff used was adjP<0.05.  Approximately 10000 genes were obtained after cutoff. Can you use rlog transformation as normalization on these 10000 genes for gene co-expression network construction. Does doing LRT test will make any ch ...
written 19 months ago by aishu.jp10
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DEseq2 sample imbalance
... I have a RNA seq data which I am trying to identify DEGs. Dataset contains Untreated - 2 replicates (time point 0hr) Treated - 4 replicates (2 replicates at 6hr and 2 replicates at 12 hr) I merged all the samples and tried to identify DEGs untreated vs treated. Is it correct to merge all samples ...
deseq written 19 months ago by aishu.jp10

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