User: pbpanigrahi

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pbpanigrahi180
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Posts by pbpanigrahi

<prev • 46 results • page 1 of 5 • next >
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Comment: C: How to get TCGA SNP in vcf and process in PLINK
... Can u post the command u typed. Also are u getting many vcf files in the output folders? Because the code generates a vcf file per tumor-normal sample pair. Are u getting only the specific error u mentioned earlier, or other error. Detailed information will help us to debug. Else provide the input f ...
written 4 months ago by pbpanigrahi180
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Answer: A: How to get TCGA SNP in vcf and process in PLINK
... Download the snp information as maf format, then you can convert maf to vcf format using [https://github.com/mskcc/vcf2maf/blob/master/maf2vcf.pl][1] [1]: https://github.com/mskcc/vcf2maf/blob/master/maf2vcf.pl ...
written 4 months ago by pbpanigrahi180
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Comment: C: CMSclassifier for colorectal cancer dataset
... You can mark the query as resolved. Thanks ...
written 4 months ago by pbpanigrahi180
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Comment: C: CMSclassifier for colorectal cancer dataset
... You can upvote the answer if you find useful. Also mark the question as resolved. ...
written 4 months ago by pbpanigrahi180
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Comment: C: CMSclassifier for colorectal cancer dataset
... Your first column in data contains id, thats why u were getting error. To resolve this try this data <- read.table("GSE103479_Normalised_matrix.txt", header = TRUE, sep = "\t") rownames(data) = data[,1]; data = data[,-1]; data_gpl <- read.table("GPL23985-23107.txt", header=TRU ...
written 4 months ago by pbpanigrahi180
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Comment: C: CMSclassifier for colorectal cancer dataset
... can u post what is there inside data and data_gpl head(data) head(data_gpl) since its row sum error, i am assuming you have non numeric entries in data. How did you import the data? Make sure data should be a dataframe with log2_scaled GEP data values, samples in columns, genes in rows, ...
written 4 months ago by pbpanigrahi180
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Answer: A: Handling values <LOD for protein intensities
... If a given protein is below LOD, limit of detection, across more than x% sample, then you can ignore. X depends on your field of study. If lets say you want to ignore a protein if it is absent/below LOD for more than 5% sample, then you ignore them. If you want to keep them, then either substitute w ...
written 4 months ago by pbpanigrahi180
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Comment: C: The rownames of demo data in MethylMix package are different from downloaded mat
... Taking average is dangerous since different clusters can have different methylation level. Did you see what results you are getting in MethylMixResults object. Can you post the object str(MethylMixResults); # if it is a data frame then head(MethylMixResults) Ultimately the methylmix wi ...
written 4 months ago by pbpanigrahi180
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Comment: C: co expression network
... Did u try what I have suggested. ...
written 4 months ago by pbpanigrahi180
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Comment: C: co expression network
... Hi Maybe Table is an internal function. I tried to search for it coexnet package, couldn't get. Anyhow if you go the [link][1], you can see in the table, its **GENE_SYMBOL** and not **GENE SYMBOL**. The geneSymbol function code has **\`GENE SYMBOL\`**. To fix this, you **manually edit** the gen ...
written 4 months ago by pbpanigrahi180

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Scholar 4 months ago, created an answer that has been accepted. For A: How to analyze a ratio data set at different replication time point.

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