User: Shamim Sarhadi

gravatar for Shamim Sarhadi
Reputation:
200
Status:
Trusted
Location:
IRAN
Last seen:
8 hours ago
Joined:
3 years, 3 months ago
Email:
b***********@gmail.com

Posts by Shamim Sarhadi

<prev • 87 results • page 1 of 9 • next >
0
votes
1
answer
188
views
1
answers
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 3 months ago by Shamim Sarhadi200
0
votes
1
answer
538
views
1
answers
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 7 months ago by Shamim Sarhadi200
0
votes
1
answer
538
views
1
answers
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 7 months ago by Shamim Sarhadi200
2
votes
1
answer
538
views
1
answer
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 7 months ago by Shamim Sarhadi200 • updated 7 months ago by assaron140
2
votes
0
answers
429
views
0
answers
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 7 months ago by Shamim Sarhadi200
15
votes
2
answers
526
views
2
answers
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 7 months ago by Shamim Sarhadi200 • updated 7 months ago by Kevin Blighe21k
0
votes
1
answer
601
views
1
answers
Comment: C: gene expression data analysis and batch effect methods
... Thank you WouterDeCoster Regards ...
written 12 months ago by Shamim Sarhadi200
1
vote
1
answer
601
views
1
answer
gene expression data analysis and batch effect methods
... I have a gene expression data including intrinsic subtypes of breast cancer, but it does not have paired normal samples, Is it possible to use normal samples from different batch if I use batch effect removal methods eg COMBAT or DWD? ...
gene expression microarray batch effect written 12 months ago by Shamim Sarhadi200 • updated 12 months ago by WouterDeCoster29k
0
votes
0
answers
839
views
0
answers
DEG analysis by limma
... Hi I have analyzed DEG between control vs sensitive to drug X, control vs insensitive to drug X, and sensitive vs insensitive. I used limma to find related DEGs, here is my codes fit <- lmFit(data, design) keep <- fit$Amean > median(fit$Amean) ebayes <- eBayes(fit[keep,], r ...
up and down regulated genes limma written 18 months ago by Shamim Sarhadi200
0
votes
0
answers
510
views
0
answers
Comment: C: Looking for a Transcriptome meta-analysis algorithm
... Hi dear spacemorrissey You can use www.networkanalyst.ca , to combine p-values obtained from different independent studies. It offers you a variety of methods e.g fisher method as a more sensitive method to combine your results. Best ...
written 18 months ago by Shamim Sarhadi200

Latest awards to Shamim Sarhadi

Popular Question 6 days ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 25 days ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 7 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 9 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 22 months ago, created a question with more than 1,000 views. For Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected
Supporter 2.3 years ago, voted at least 25 times.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics for a medical student with interest in genetics
Scholar 2.3 years ago, created an answer that has been accepted. For A: Bioinformatics for a medical student with interest in genetics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1987 users visited in the last hour