User: prithvi.mastermind

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Posts by prithvi.mastermind

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UCSC Xena Probe to Gene mapping
... I have retrieved TCGA raw read counts from UCSC Xena for oral cancer. List of Ensembl IDs is present in the counts file. The UCSC Xena browser also provides a file at the same link consisting the Ensembl IDs from expression file and their corresponding Gene Symbols. There are many instances where a ...
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Comment: C: DESeq2 Batch correction enquiry?
... Thanks, Kevin. Before creating the DESeQ object i read my data like this. Count_data <- read.table(file = "BRCA_DESeQ.txt", header = T, sep = "\t") CC <- (Count_data[,2:1218]) Col_data = read.table(file = "COL.txt", header = T, sep = "\t") dds = DESeqDataSetFromMatrix(countDat ...
written 7 days ago by prithvi.mastermind0 • updated 7 days ago by genomax85k
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Comment: C: DESeq2 Batch correction enquiry?
... I completely understand the idea of the respective forum sir, but i'm a complete beginner in R and trying to dig in the concepts. Help from your end would be a great motivation for me. i framed this code after reading: dds <- DESeqDataSetFromMatrix(countData = CC, colData = Col_data, design ...
written 7 days ago by prithvi.mastermind0 • updated 7 days ago by Kevin Blighe61k
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Comment: C: DESeq2 Batch correction enquiry?
... Sir after running this step # normalise dds <- DESeq(dds) How can I normalize and log-transform the data? Please help rld <- rlogTransformation(dds) # for rlog transormation norm_counts = counts(rld, normalized = TRUE) #for normalization Is this step relevant? ...
written 7 days ago by prithvi.mastermind0 • updated 7 days ago by genomax85k
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Comment: C: DESeq2 Batch correction enquiry?
... Thank you sir for your help. But how can i save expression data that has been batch corrected after running the last command: assay(vsd) <- limma::removeBatchEffect(assay(vsd), colData(dds)[['batch']]) ...
written 8 days ago by prithvi.mastermind0
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Comment: C: DESeq2 Batch correction enquiry?
... Thank you sir for your prompt response. No this is not my script. Its an example script from DESEq2 page which I ran for understanding the concept. the vsd$batch is showing NULL. what does this mean? ...
written 11 days ago by prithvi.mastermind0
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DESeq2 Batch correction enquiry?
... I'm using DESEq2 package for obtaining normalized data from raw read counts of RNA-Seq data. I'm not interested to do any downstream analysis like DEGs identification and just want the normalized and transformed expression matrix. In the steps, I also incorporated the following for any batch effect. ...
software error R next-gen rna-seq written 11 days ago by prithvi.mastermind0 • updated 11 days ago by ATpoint36k
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HIPPIE Protein Database Query
... I'm interested to do PPI network analysis using HIPPIE database. On the home-page of HIPPIE it states the following: A threshold on the HIPPIE confidence score can be chosen. The user can either specify a custom value between 0 and 1 or choose a predefined confidence level: medium confidence (0.63 ...
software error gene written 6 weeks ago by prithvi.mastermind0
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Enrichr Result analysis interpretation ?
... I'm using Enrichr GUI version for pathway enrichment analysis. I compiled the results from various Enrichr geneset libraries like BioCarta, WikiPathways, KEGG, Reactome, Panther, etc. The result sheets of all these libraries are having adjusted p-values = 1 only, while there is some variation in nom ...
gene software error written 6 weeks ago by prithvi.mastermind0 • updated 6 weeks ago by dsull1.4k

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