User: vignesh

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vignesh90
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Posts by vignesh

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Ensembl id to GeneSymbol with biomart
... Hello, I have 3224 Ensembl id's as rownames in a dataframe "G". To convert Ensembl ids into Genesymbols I used biomart like following. library('biomaRt') mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) genes <- rownames(G) G <-G[,-6] G_list <- getBM( ...
biomart written 3 months ago by vignesh90 • updated 3 months ago by sandeep.amberkar180
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Comment: C: How to calculate RPKM from featureCounts output
... Hello, Yes I used "#" for the Geneid as you showed in the example. But still I didn't get the sample names in my output. But based on input data can I replace "0" with sample names? ...
written 3 months ago by vignesh90
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Comment: C: How to calculate RPKM from featureCounts output
... Ok. I saved the file now in tab-delimited and looks like it worked. I didn't get any error. But I don't understand why the Sample names are missing. Geneid 0 0 0 0 0 0 Length ENSG00000000003 2.245105716 3.553743948 1.681000503 2.734256037 0.640389439 2.830847732 11231 ENSG0000000000 ...
written 3 months ago by vignesh90
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Comment: C: How to calculate RPKM from featureCounts output
... I save the file now into tab-delimited "sample_count_test.count". I got the following error after giving the command. Illegal division by zero at rpkm_script_beta.pl line 44, <> line 66. ...
written 3 months ago by vignesh90
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Comment: C: How to calculate RPKM from featureCounts output
... HEllo, As you mentioned above my data input is given as following: #Geneid STB32 STB34 STB36 STB40 STB65 STB79 Length ENSG00000000003 1247 1938 1121 1307 379 1920 11231 ENSG00000000005 0 15 34 7 1 3 15678 ENSG00000000419 1420 1874 1684 915 2431 1603 18768 ENSG0000000045 ...
written 3 months ago by vignesh90
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Comment: C: How to define the gene length for RPKM calculation
... Dear Michael, I have to calculate rpkm from counts data which I got from STAR. I'm using edgeR for this and it needs gene_length. I'm doing this rpkm calculation not for DE analysis. Could you please tell me how can I calculate rpkm from counts. Do you think this is the right way to calculate gen ...
written 3 months ago by vignesh90
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Thankyou Tris. I have an other question. How to check the survival for High and Low expression of a gene? I have gene expression data of TP53 and divided the samples into two groups i.e. High expression and low expression. So, with this I want to see the survival b/w High and low. With your above co ...
written 5 months ago by vignesh90
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Hello, Thanks for putting the code in github. I have seen the just now. But Could you please tell how to use this code for Disease free survival plot? Thank you ...
written 5 months ago by vignesh90
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... for (i in 1:dim(new_tum)[1]){ if ( sum ( is.na(new_tum[i,])) < dim(new_tum)[2]){ m <- min(new_tum[i,],na.rm=T) new_tum_collapsed <- c(new_tum_collapsed,m) } else { new_tum_collapsed <- c(new_tum_collapsed,'NA') } } You should ope ...
written 5 months ago by vignesh90
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Answer: A: [RNAseq] Do anyone have already-built Hisat2 indexes files for human genome (GRC
... Here you can get Indexes for human genome and also other (https://ccb.jhu.edu/software/hisat2/index.shtml) ...
written 5 months ago by vignesh90

Latest awards to vignesh

Popular Question 15 days ago, created a question with more than 1,000 views. For How to build Hisat2 index for human genome (GRCh37 )?
Centurion 8 weeks ago, created 100 posts.
Supporter 5 months ago, voted at least 25 times.

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