User: Shamim Sarhadi

gravatar for Shamim Sarhadi
Reputation:
210
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IRAN
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1 day, 1 hour ago
Joined:
4 years, 1 month ago
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Posts by Shamim Sarhadi

<prev • 91 results • page 1 of 10 • next >
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Binary mutation data format
... Hi I want to run a package named [DawnRank][1] in R. This package has some data requirements and file format. One of these requirements is a mutation file that the rows represent the genes and the columns represent the sample IDs and the mutation for each gene in each samples are binary (0,1) (yo ...
R mutation data tcga dawnrank written 11 days ago by Shamim Sarhadi210 • updated 10 days ago by igor7.6k
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Estimating the purity of tumor cells in gene expression microarray data
... Hi Is there any tool for defining the tumor cell purity in gene expression microarray data? Thanks in advance ...
cell purity microarray written 8 months ago by Shamim Sarhadi210
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Longitudinal breast cancer data
... Hi I am looking for the longitudinal breast cancer data. These data ideally should have two or more sampling time point from primary tumor in one patient. Those would be great when they have transcript and genomic data. Do you know any open source data repository for this kinds of data I know tha ...
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Answer: A: How to optimize the homology modeling?
... There are several tools that you could refine your 3D model e.g. [TIGRESS][1], [PREFMD][2] that use different methodological approaches to refine the protein structure models. [1]: http://atlas.engr.tamu.edu/refinement/ [2]: https://feig.bch.msu.edu/web/services/prefmd/ ...
written 9 months ago by Shamim Sarhadi210
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Comment: C: Gene expression study
... Dear c.chakraborty, if you want to do a gene expression meta-analysis eg between case and control you need to select studies that have case and paired control samples and you could not compare cases from one study and controls from different study because of huge noise and batch to batch variation b ...
written 14 months ago by Shamim Sarhadi210
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Comment: A: Cut-off for genesets in GSEA
... Excluding gene sets with fewer that 15 is default of GSEA not my cut-off !! honestly it's still puzzling for me, I think, I should read the GSEA user guide again and consider your notes Thank you Mark ...
written 17 months ago by Shamim Sarhadi210
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Comment: C: Cut-off for genesets in GSEA
... Hi Mark thank you for your answer I Know about cut-off for the DEGs, but precisely my question is about cut-offs for the genesets that must be include or exclude by GSEA , in "Basic field setting" of GSEA there are two options about size of genesets that must be considered in its analysis and I don' ...
written 17 months ago by Shamim Sarhadi210
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Cut-off for genesets in GSEA
... Hi I'm running GSEA on my pre-ranked genes consisting 260 differentially expressed genes following GSEA instructions, but it is obscure for me how to set max and min size for exclude gene set. In GSEA user guide it's noticed that "defaults that are appropriate for datasets with 10,000 to 20, ...
gsea written 17 months ago by Shamim Sarhadi210 • updated 17 months ago by assaron170
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Gene set enrichment analysis
... Hi I run GSEA on a pre-ranked (according to the log fold changes values) gene list that obtained from a DEG analysis between healthy and cancer samples, after GSEA I used significant geneset for leading edge analysis, but the result is ambiguous !! I attached one of leading edge clustergrams [here][ ...
deg analysis gsea enrichment analysis written 17 months ago by Shamim Sarhadi210
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7 follow
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Reporting p.value for my PCA results
... Hi I've done PCA for my gene expression data after DEG analysis, I can see that my case and control samples clustered distinctly but **I want to report a p.value for this result**, it worth to notice that I have the coordinate csv file that represents coordinates of samples from different phenotype ...
gene expression pca written 18 months ago by Shamim Sarhadi210 • updated 18 months ago by Kevin Blighe41k

Latest awards to Shamim Sarhadi

Great Question 10 months ago, created a question with more than 5,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 10 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 11 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 17 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 19 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 2.3 years ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected
Supporter 3.1 years ago, voted at least 25 times.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics for a medical student with interest in genetics
Scholar 3.1 years ago, created an answer that has been accepted. For A: Bioinformatics for a medical student with interest in genetics

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