User: Momeneh Foroutan

Reputation:
10
Status:
New User
Location:
Australia
Last seen:
3 years, 6 months ago
Joined:
4 years, 5 months ago
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s*************@gmail.com

Posts by Momeneh Foroutan

<prev • 9 results • page 1 of 1 • next >
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Obtaining clean data after adjusting for batch effects using SVA
... Hi all (and Andrew Jaffe), I know there is a post related to this topic here "https://support.bioconductor.org/p/47350/" but I actually have a question about the answer given by Andrew to that post. Andrew has kindly suggested using the below function to obtain the clean data adjusted for surrogat ...
sva written 3.5 years ago by Momeneh Foroutan 10
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Comment: C: SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod
... Hi Ying, I remember I had the same issue with one of my datasets... were you able to find a way to solve this problem? You should have the same size for rows in you pheno data and columns in you expression matrix. Cheers,   ...
written 3.5 years ago by Momeneh Foroutan 10
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Answer: A: Dealing with the output of ssGSEA method from GSVA package
... It seems that there was a problem with my code! I should use the below code instead: gsva(m, list(genes= geneSet), method="ssgsea", mx.diff=1, verbose=FALSE, parallel.sz=1) And it gives me ES :-) Thanks anyway! Sepideh   ...
written 3.8 years ago by Momeneh Foroutan 10
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Dealing with the output of ssGSEA method from GSVA package
... Hi all, I've used GSVA package (many thanks to the developers of the package) and I got a very nice ES by using the "gsva" method from the package but I was a bit surprised that it did not give me the final ES for "ssgsea" method... I have a matrix m (18000 genes in row and 600 patient samples in c ...
gsva ssgsea written 3.8 years ago by Momeneh Foroutan 10
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Comment: C: Error in running gsva function from GSVA package
... Many thanks Robert, In fact, it solved the problem :-) I don't get the error anymore... however, I get warnings and I am not sure whether I should be worried about them? The warnings say that I have some genes with constant values across all samples. Please look at them: By running "gsva" method, ...
written 3.8 years ago by Momeneh Foroutan 10
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Error in running gsva function from GSVA package
... Hi all, I have a gene signature (about 300 genes) including up- and down-regulated gene sets, and would like to use package GSVA to assess my signature on samples from a matrix (18000 genes in row and 600 patient samples in columns). The row names of the matrix as well as the gene sets are both gen ...
gsva written 3.8 years ago by Momeneh Foroutan 10 • updated 3.8 years ago by Robert Castelo2.3k
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Comment: C: How to mport publically available RMA processed dataset (on ArrayExpress) into L
... Thanks James for that all, I downloaded the data in the same way you showed here, however, the data is RMA normalized and I cannot obtain eset by doing rma() on the dataset which is already normalized. Regards, Sepideh ...
written 4.5 years ago by Momeneh Foroutan 10
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Comment: C: How to mport publically available RMA processed dataset (on ArrayExpress) into L
... Thank you Aaron, I did not think that we can import something other than exprSet object into it because Gordon Smyth has mentioned in his paper "http://www.statsci.org/smyth/pubs/limma-biocbook-reprint.pdf" that "the object eset is assumed to be of class exprSet containing normalized probe-set log-i ...
written 4.5 years ago by Momeneh Foroutan 10
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How to mport publically available RMA processed dataset (on ArrayExpress) into Limma?
... Hi there, I have a processed microarray dataset (HG-U133A) downloaded from the ArrayExpress. The authors have processed the data using RMA in affy package and only the processed data is available. What I have now is a spreadsheet containing a summary of normalized expression values. I know that for ...
microarray limma written 4.5 years ago by Momeneh Foroutan 10 • updated 4.5 years ago by Aaron Lun24k

Latest awards to Momeneh Foroutan

Popular Question 3.5 years ago, created a question with more than 1,000 views. For Dealing with the output of ssGSEA method from GSVA package
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to mport publically available RMA processed dataset (on ArrayExpress) into Limma?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Dealing with the output of ssGSEA method from GSVA package
Scholar 3.8 years ago, created an answer that has been accepted. For A: Dealing with the output of ssGSEA method from GSVA package

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