User: fp89

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fp8920
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Posts by fp89

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Survival analysis: data clinical and pathways
... Hello, I need to perform survival analysis to find significant associations of specific pathway activities to patient survival. I'm trying to perform the analysis using this tutorial https://github.com/mforde84/RNAseq-Survival-Analysis-TCGA-KIRC/blob/master/survival_rnaseq_analysis.R. I have two f ...
R data clinical survival analysis pathways written 20 months ago by fp8920 • updated 20 months ago by zx87549.6k
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Comment: C: Help with multiple batch effects
... thank you...These are my clustering for [group][1], [plateId][2] and [TSS][3]. [1]: https://ibb.co/imDm6d [2]: https://ibb.co/dgkSCJ [3]: https://ibb.co/m0bW6d ...
written 2.2 years ago by fp8920
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Comment: C: Help with multiple batch effects
... Hi, I'm a bit confused. How can I detect the presence of batch effects? With PCA ok but how can I interpret the graph? This is [my pca][1] . Red tumor and blue normal samples. [1]: https://ibb.co/bJPL9y ...
written 2.2 years ago by fp8920
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Comment: C: Help with multiple batch effects
... Hi Kevin, thank you. This page [mdanderson][1] suggests different batch types. [1]: http://bioinformatics.mdanderson.org/tcgambatch/ ...
written 2.2 years ago by fp8920
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Help with multiple batch effects
... Hello, I have an expression matrix of 1208 samples (1095 tumor and 113 normal) downloaded from TCGA. I know there are 3 batch effects: type, plateId and TSS. I've tried to correct for them with Combat but I need a little help with the model.matrix. batch<-as.data.frame(cbind(samples,plateI ...
sva batch effects combat written 2.2 years ago by fp8920 • updated 2.2 years ago by genomax89k
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(Closed) Filtering a matrix for the same value
... Hello, I have a matrix with samples in columns, pathways names in rows and p values in each cell. I would like to subset the matrix based on the cell values, e.g cell <0.05. I've tried to do it using this function. Is it correct? Thanks in advance. matrix_filt<-matrix[which(matrix<0.05), ...
R written 2.3 years ago by fp8920
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Problem with Pathways
... Hi, I have two files (A and B): one is a list of circuit pathways with circuit_id, hgnc and entrez_id; the other one is an expression matrix with samples (50 normal samples and 50 tumor samples) in columns and significative pathways in rows (1094). I converted them into two dataframes, the first one ...
pathway merge dataframe rstudio circuit pathway written 2.8 years ago by fp8920 • updated 2.8 years ago by genomax89k
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Comment: C: How can I replace pathway names with gene names?
... I have 100 samples (50 tumor and 50 normal) and 1014 significative circuits. I have to find genes included in each subpathway (circuit) so I can obtain expression values for each gene in each sample. I need to cross the two dataframes. Can I do it with merge function? And if so, how? Many thanks Gli ...
written 2.9 years ago by fp8920
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How can I replace pathway names with gene names?
... Hi,I'm bioinformatics student. I have two dataframes (A and B) and I want to convert the row names of the B with hgnc of the A but I don't know how I can do that. I tried with row.names(B)<-A$hgnc but the following message appears: Error in `row.names<-.data.frame`(`*tmp*`, value = c("MAPK1", ...
pathway R row names gene names written 2.9 years ago by fp8920

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