User: prithvi.mastermind
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Posts by prithvi.mastermind
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... 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 ...
written 1 day ago by
prithvi.mastermind • 0
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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.mastermind • 0
• updated
7 days ago by
genomax ♦ 85k
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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.mastermind • 0
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7 days ago by
Kevin Blighe ♦ 61k
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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.mastermind • 0
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7 days ago by
genomax ♦ 85k
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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.mastermind • 0
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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.mastermind • 0
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... 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. ...
written 11 days ago by
prithvi.mastermind • 0
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11 days ago by
ATpoint ♦ 36k
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... 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 ...
written 6 weeks ago by
prithvi.mastermind • 0
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... 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 ...
written 6 weeks ago by
prithvi.mastermind • 0
• updated
6 weeks ago by
dsull • 1.4k
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