User: Shamim Sarhadi

gravatar for Shamim Sarhadi
Reputation:
180
Status:
Trusted
Location:
IRAN
Last seen:
36 minutes ago
Joined:
2 years, 8 months ago
Email:
b***********@gmail.com

Posts by Shamim Sarhadi

<prev • 86 results • page 1 of 9 • next >
0
votes
1
answer
116
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 9 days ago by Shamim Sarhadi180
0
votes
1
answer
116
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 9 days ago by Shamim Sarhadi180
1
vote
1
answer
116
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 9 days ago by Shamim Sarhadi180 • updated 7 days ago by assaron100
1
vote
0
answers
125
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 17 days ago by Shamim Sarhadi180
15
votes
2
answers
189
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 29 days ago by Shamim Sarhadi180 • updated 29 days ago by Kevin Blighe7.3k
0
votes
1
answer
313
views
1
answers
Comment: C: gene expression data analysis and batch effect methods
... Thank you WouterDeCoster Regards ...
written 6 months ago by Shamim Sarhadi180
1
vote
1
answer
313
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 6 months ago by Shamim Sarhadi180 • updated 6 months ago by WouterDeCoster23k
0
votes
0
answers
529
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 11 months ago by Shamim Sarhadi180
0
votes
0
answers
352
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 11 months ago by Shamim Sarhadi180
0
votes
1
answer
417
views
1
answers
Comment: C: A question about adjust-pvalue in gene expression analysis
... Hi Dear Farbod, yes and I corrected my mistake Thanks for your explanation, I want to compare two biological states that I think they are very near to each other, and I want to find DEG's that contribute to biological mechanisms that led to transition between these two states, according your comment ...
written 13 months ago by Shamim Sarhadi180

Latest awards to Shamim Sarhadi

Popular Question 15 days ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 11 weeks ago, created a question with more than 1,000 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 16 months ago, created a question with more than 1,000 views. For Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected
Supporter 20 months ago, voted at least 25 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics for a medical student with interest in genetics
Scholar 20 months 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: 1389 users visited in the last hour