User: nia

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nia10
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Posts by nia

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Comment: C: Absence of significant gene in DEG list
... I have updated the post ...
written 18 months ago by nia10
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Absence of significant gene in DEG list
... Dear all, I am a biologist and currently working on the identification of DEGs from a raw data which has about 50 thousand genes and after applying statistics on that I have come up with about 250 genes but the problem is that, the DEGs which have been identified by using packages of bioconductor m ...
microarray limma written 18 months ago by nia10 • updated 18 months ago by Aaron Lun25k
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Comment: C: Microarray analysis of .idat files to identify degs
... Dear jaro, Thankyou for the help. I got the desired results by following below code, I design the code as per my understanding. Kindly have a look on the code. library(limma) idatfiles = dir(pattern = ".idat") bgxfile = dir(pattern = ".bgx") data = read.idat(idatfiles, bgxfile) datanorm <- neqc ...
written 20 months ago by nia10
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Comment: C: Microarray analysis of .idat files to identify degs
... Thankyou for your response I used code given below but its generating error. CODE library(limma) idatfiles = dir(pattern = ".idat") bgxfile = dir(=pattern = ".bgx") data = read.idat(idatfiles, bgxfile) datanorm <- neqc(data) #design matrix   f <- factor(datanorm$Condition, levels = unique(data ...
written 20 months ago by nia10
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Comment: C: Boxplot and Identification of DEG
... Dear Aaron, First of all  thank you my concepts are much clear now it such a detailed information. As you said 0.5 is not a good score but can you suggest me what should I do because when I choose 0.05 FDR score it shows me no result. I also optimized the result by following FDR score: FDR score ...
written 23 months ago by nia10
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Boxplot and Identification of DEG
...   Dear Fellows, I have 2 questions I hope from your precious time you will try to solve my queries: 1) Firstly my dataset is already processed it is not RAW. So I retrieved boxplot of samples successfully by using R. Then next day I identified DEGs by using LIMMA and GEOquery packages and the adj ...
biobase limma geoquery written 23 months ago by nia10 • updated 23 months ago by Aaron Lun25k
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FUNCTIONAL ENRICHMENT ANALYSIS
... Dear fellows, I need your suggestion i have around 200 degs which i retrieved after doing its linear modeling , i submit the genes in (genecodis3) tool for the biological and molecular enrichment analysis and i got around 250 GO annotations is it fine i just take top 10 for table (fdr<0.05) (tes ...
fdr genecodis3 written 2.5 years ago by nia10 • updated 2.5 years ago by Robert Castelo2.3k
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Comment: C: fdr score for degs
... thankyou so much i got the point ...
written 2.5 years ago by nia10
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fdr score for degs
... hello fellows!!!!!!!!!!! i have 10 samples from Geo data set  and there was 1067 probe ids its showed (pvalue<0.05) was set  after applying limma code (fdr < 0.5) was set , then 294 probeids with genes symbol and with all the other relevant info. was retrieved from 294 113 was upreg and 181 w ...
fdr deg written 2.5 years ago by nia10 • updated 2.5 years ago by svlachavas740
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Answer: A: microarray analysis code
... Thank you James for your response it was really helpful, i am getting this error now . plotPCA(eset, groups =as.numeric(pData(Data)[,1]),groupnames =levels(pData(Data)[,1])) > grp [1] 1  2  3  4  5  6  7  8  9  10 Levels: 1 10 2 3 4 5 6 7 8 9 > design <- model.matrix(~grp) > design   ...
written 2.5 years ago by nia10

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Popular Question 18 months ago, created a question with more than 1,000 views. For how to use log2 transformation and limma

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