User: deathmagnetic20

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Posts by deathmagnetic20

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Beta values of methylation data: mean or median? how to create an event?
... I have filtered in R a Illumina Human Methylation 450K data into a data frame of my cg's of interest. Look like this: head(x_filtered[1:3]) TCGA-WB-A81T-01A TCGA-WB-A81G-01A TCGA-WB-A815-01A cg12150457 0.12335296 0.10067159 0.13113157 cg07035961 ...
R tcga methylation illumina written 7 weeks ago by deathmagnetic2010
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Comment: C: How to reproduce a stacked bar chart in R
... Yes with my low code level, sorry! I meant I dont know how to include all the barcodes and cell types but manually. ...
written 8 weeks ago by deathmagnetic2010
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Comment: C: How to reproduce a stacked bar chart in R
... I will try it, thanks! Challenging, cause I have to include 178 rows (barcodes) and 28 (cell types). Is there a simple code to do it? ...
written 8 weeks ago by deathmagnetic2010
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Comment: C: How to reproduce a stacked bar chart in R
... Thank you! My problem is that I have a table data format like this one, so I dont know how to reorder in order to have the columns you said: ![enter image description here][1] [1]: https://i.ibb.co/7VS9WPs/Captura-de-pantalla-2020-11-26-a-las-21-18-22.png ...
written 8 weeks ago by deathmagnetic2010
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Comment: C: How to reproduce a stacked bar chart in R
... Reposted the image, sorry! ...
written 8 weeks ago by deathmagnetic2010
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How to reproduce a stacked bar chart in R
... Hi, I have used the analytical tool CIBERSORTx to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using RNAseq and TCGA data. The output table have TCGA barcodes in rows, and cell types in columns. I would like to generate ...
R rna-seq written 8 weeks ago by deathmagnetic2010 • updated 8 weeks ago by bioinformatics2020570
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Comment: C: Obtaining the z-score in only tumor RNAseq data
... I agree. The problem is that scaling per gene extremely stratify the samples (after create an event vector) over the median expression gene of interest value, so almost the entire samples are "high expression". I'm not completely sure if global z-score is a bad practice for survival analysis with g ...
written 9 months ago by deathmagnetic2010
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Comment: C: Obtaining the z-score in only tumor RNAseq data
... Thank you very much Kevin, your reply has been very helpful to me. I have been doing some research and I still don't know why one approach would be more favorable rather than the other one. Scaling by row shows me very low expression values, so I tried by global and I get a median z-score of my ge ...
written 9 months ago by deathmagnetic2010
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Obtaining the z-score in only tumor RNAseq data
... Hi Biostars community, I am currently doing survival and other analyses in RNAseq gene expression data using the ACC TCGA database. How can i change the code for obtaining the z-score applying this formula? > z = [(value gene X in tumor Y)-(mean gene X in tumor)]/(standard > deviation X in ...
gene R rna-seq written 9 months ago by deathmagnetic2010 • updated 9 months ago by Kevin Blighe69k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Hi TriS and community, Thank you so much for this tutorial, it is being extremely helpful and insightful to me. How can i change the code for obtaining the z-score scal <- function(x,y){ mean_n <- rowMeans(y) # mean of normal sd_n <- apply(y,1,sd) # SD of normal ...
written 9 months ago by deathmagnetic2010

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