User: aishu.jp

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aishu.jp20
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Posts by aishu.jp

<prev • 10 results • page 1 of 1 • next >
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How to perform DEseq2 on datasets without replicates or merged replicates
... I have a plant RNA seq data of control and treated conditions obtained from 4 different days. This SRA dataset obtained from NCBI doesn't have replicates but have mentioned in their article that they have merged the biological replicates drawn during sequencing process in the sample preparation sect ...
deseq2 R bioconductor replicates rna_seq written 3 days ago by aishu.jp20 • updated 2 days ago by swbarnes2340
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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 5 months ago by aishu.jp20
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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 5 months ago by aishu.jp20
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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 5 months ago by aishu.jp20 • updated 5 months ago by swbarnes2340
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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 10 months ago by aishu.jp20 • updated 10 months ago by Michael Love26k
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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 17 months ago by aishu.jp20
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Comment: C: DESeq LRT test and construction of Co-expression network
... Thank you for helping me ...
written 20 months ago by aishu.jp20
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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 20 months ago by aishu.jp20 • updated 20 months ago by Peter Langfelder2.3k
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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 20 months ago by aishu.jp20
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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 21 months ago by aishu.jp20

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