User: Shamim Sarhadi

gravatar for Shamim Sarhadi
Reputation:
170
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Location:
IRAN
Last seen:
1 week ago
Joined:
2 years, 6 months ago
Email:
b***********@gmail.com

Posts by Shamim Sarhadi

<prev • 81 results • page 1 of 9 • next >
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Comment: C: gene expression data analysis and batch effect methods
... Thank you WouterDeCoster Regards ...
written 4 months ago by Shamim Sarhadi170
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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 4 months ago by Shamim Sarhadi170 • updated 4 months ago by WouterDeCoster21k
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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 9 months ago by Shamim Sarhadi170
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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 9 months ago by Shamim Sarhadi170
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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 11 months ago by Shamim Sarhadi170
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A question about adjust-pvalue in gene expression analysis
... Hi I am doing a meta-analysis with some publicly available datasets, I want to finding DEG's between case and control in my datasets seperately and then combine the p-valu's , but in some of my dataset with adjust-pvalue less than 0.05 , there is not any DEGs , now I think I have two options, 1- Inc ...
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Protein modelling with modeller
... Hi I am a newbie in protein modeling, I create a model for my aa sequence with modeller and I-TASSER (zhang lab server), now I have two models with different sequence, the model from I-TASSER has the same sequence with my target ,but the model from Modeller has different sequence in some area of seq ...
proteing modeling modeller written 14 months ago by Shamim Sarhadi170
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CEL file to expressionSet
... Hi I have 2500 CEL files, I put them in my work directory and then I ran `ReadAffy`()`, but It gave me "cannot allocate vector of size of... error , I've tried with 500 CEL file and I gave the same error again, let me know about your experience in this case Thanks in advance ...
affy cel expressionset written 15 months ago by Shamim Sarhadi170
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Which one of protein modeling programs is better?
... Hi I want to know,which one of protein modeling programs is better,based on your experience. I've searched,but there is a lot of conflicts !!!!, I-tasser,modeller,TSP-PRED and... ...
protein modelling written 15 months ago by Shamim Sarhadi170
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Comment: C: Retrieving gene names from list of mRNA accession IDs
... Bionetdb is a helpful tool for ID conversions https://biodbnet-abcc.ncifcrf.gov/db/db2db.php ...
written 15 months ago by Shamim Sarhadi170

Latest awards to Shamim Sarhadi

Popular Question 22 days ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 8 months ago, created a question with more than 1,000 views. For cannot allocate vector of size 64.1 Mb
Popular Question 14 months ago, created a question with more than 1,000 views. For Error in `[.data.frame`(pData(eset), , symLabel) : undefined columns selected
Supporter 18 months ago, voted at least 25 times.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics for a medical student with interest in genetics
Scholar 18 months ago, created an answer that has been accepted. For A: Bioinformatics for a medical student with interest in genetics

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