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... 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,], robust=TR ...
written 21 months ago by Shamim Sarhadi20 • updated 21 months ago by Aaron Lun21k
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... Hi  Steve Lianoglou Could you please explain for me , how can I find down regulated genes in each phenotype? Thank you very much ...
written 21 months ago by Shamim Sarhadi20
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... Thank you very much colnames(design) [1] "(Intercept)"                                            "factor(sensitivity$chemosensitivity)Rx Sensitive" According on your explanation the log fold change correspond to Rx Sensitive ,In my case log fold change= - 0.87 this negative log fold change is re ... written 21 months ago by Shamim Sarhadi20 1 answers 362 views 1 answers ... Thank you for your reply ​design <- model.matrix(~factor(data$chemosensitivity)) factor(data$chemosensitivity) [1] Rx Sensitive Rx Sensitive Rx Insensitive Rx Insensitive Rx Insensitive ... Levels: Rx Insensitive Rx Sensitive fit <- lmFit(data, design) keep <- fit$A ...
written 21 months ago by Shamim Sarhadi20
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... Hi I use limma to find DEGs between chemo-resistance and chemo-sensitive samples, in limma output I found that e.g one of my genes has log fold change= - 0.87, Now I have a question, Does this down regulation happened in my chemo-resistance or chemo-sensitive samples? It worth to notice that I don ...
written 21 months ago by Shamim Sarhadi20 • updated 21 months ago by Steve Lianoglou12k
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...  Thank you James W. MacDonald I think genefilter is better for my application. all the best ...
written 23 months ago by Shamim Sarhadi20
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... Thank you  James W. MacDonald Please correct me if I'm wrong, using genefilter in this case just help us to remove redundant prob-id's or those that have not expressed from a pre-defined cut-off while here for summarization we need to do something like calculating mean of peopsets to converting pro ...
written 23 months ago by Shamim Sarhadi20
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... I am using fRMA to preprocess my affy dataset from  hgu133a2 platform and I am getting a dataset with 54k unique probe id's in the eSet format, but I need to have a dataset with unique gene symbol or ENTREZID , as you know in the frma output there are a lot of prob ids that map to a gene Id , how ca ...
written 23 months ago by Shamim Sarhadi20 • updated 23 months ago by James W. MacDonald47k
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... Hi I am using sigcheck package to validate my signature I run these codes library(breastCancerNKI) library(SigCheck) data(nki) data(knownSignatures) nki <- nki[,!is.na(nki\$e.os)] check <- sigCheck(nki, classes="e.os", survival="t.os",signature=mysignature,annotation="HUGO.gene.symbol",valid ...
written 2.2 years ago by Shamim Sarhadi20
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... Hi Rory Stark I am grateful for your nice package sigcheck, I am using this package to test my signature, but I have a problem, it is very time consuming,I think it is better to tell you more about my signature, it has 98 genes and I test its performance in some independent studies, and also I chec ...
written 2.2 years ago by Shamim Sarhadi20

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