User: Gema Sanz

gravatar for Gema Sanz
Gema Sanz50
Reputation:
50
Status:
New User
Location:
Karolinska Institutet
Last seen:
3 months, 3 weeks ago
Joined:
4 years, 9 months ago
Email:
g*******@gmail.com

about me

Posts by Gema Sanz

<prev • 29 results • page 1 of 3 • next >
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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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 4 months ago by Gema Sanz50
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How to calculate moderated z-score (MODZ)
... Hi, I'm trying to reproduce the calculation of moderated z-score (MODZ) described in PMID: 29195078 for some microarray data. Calculation is described as follows: > Replicate-consensus signatures (MODZ) L1000 experiments are typically > done in 3 or more biological replicates. We derive a c ...
z-score modz written 4 months ago by Gema Sanz50 • updated 4 months ago by Devon Ryan81k
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Comment: C: correlation between genes
... Hi, following this discussion, I've been trying to use cor() after transposing my gene/samples matrix from microarray experiment (so genes are as columns and samples are as rows) but I'm not sure how to define "y", I get this error: cor<- cor(tm, use="pairwise.complete.obs","spearman") E ...
written 4 months ago by Gema Sanz50

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For WGBS data analysis in Galaxy?

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