User: Gema Sanz

gravatar for Gema Sanz
Gema Sanz70
Reputation:
70
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Trusted
Location:
Karolinska Institutet
Last seen:
6 months, 1 week ago
Joined:
6 years, 1 month ago
Email:
g*******@gmail.com

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Posts by Gema Sanz

<prev • 31 results • page 1 of 4 • next >
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Read TCGA BAM files into TEtranscripts tool (python) without downloading them?
... Hi, I wonder if there is any way to read TCGA bam files into linux console to analyze them without need of downloading them. For example, I want to use TEtranscripts from [TEToolkit][1] to analyze quite large amoung of TCGA samples but I'm not sure if I could skip the downloading step due to the sp ...
linux tcga rna-seq bam written 6 months ago by Gema Sanz70
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Error creating pool for permutation test (PeakPermTest from ChipPeakAnno)
... Hi, I want to run permutation test to see the significance of the overlap for my chip-seq datasets. I'm following this example to remove blackspots and create the pool: data(HOT.spots) data(wgEncodeTfbsV3) hotGR <- reduce(unlist(HOT.spots)) removeOl <- functio ...
permutation chippeakanno chip-seq written 16 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... I think it is working! The function doesn't give errors and I got something that I think is the expected output https://ibb.co/eLtkSc ...
written 21 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... wow, thanks A LOT!!! this is a start point, I will play around with it! :) ...
written 21 months ago by Gema Sanz70
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Answer: A: How can I analyze microarray and RNA-Seq data from TCGA?
... You can work directly with the data from cBioPortal, they provide microarray data as z-scores, which is normalized expression data (is the number of standard deviations from the mean a data point is). You can use it directly with the tools provided in cBioPortal or download it to do your own heatmap ...
written 21 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... Thanks! that solved the "y" problem. As I wrote above what I need to get according to the description of the calculation, is a correlation value per gene in each sample, and the output from cor() is only one correlation value per gene pair, I'm not sure how to get that, I guess I should do a correla ...
written 21 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... Sorry, I reached the limit of coments per 6h... this is an example matrix of my data, I have 6 different samples and 928 genes, it is already trasposed https://imgur.com/a/iZtsm what I need to get according to the description of the calculation, is a correlation value per gene in each sample, and ...
written 21 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... yes it was me, but I wanted to post the whole thing to make things clear about what I need to do ...
written 21 months ago by Gema Sanz70
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Comment: C: How to calculate moderated z-score (MODZ)
... I just get the same error with that code. The only way I found to skip that error and make the code work is to set y as tm, but I don't know the meaning of that y<- tm cor<- cor(tm, y, use="pairwise.complete.obs","spearman") ...
written 21 months ago by Gema Sanz70
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Comment: C: correlation between genes
... it is a matrix already, I did tm <- as.matrix(tm) but the only way to avoid the error is if I set "y<-tm", then I get a correlation table of 900x900 with the correlation of each gene with every other gene but I'm not sure what I'm comparing because y should be 6 samples... I don't know ...
written 21 months ago by Gema Sanz70

Latest awards to Gema Sanz

Popular Question 16 months ago, created a question with more than 1,000 views. For WGBS data analysis in Galaxy?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For WGBS data analysis in Galaxy?

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