User: nia

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nia0
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Posts by nia

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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 1 day ago by nia0 • updated 19 hours ago by Aaron Lun17k
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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 6 months ago by nia0 • updated 6 months ago by Robert Castelo2.0k
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Comment: C: fdr score for degs
... thankyou so much i got the point ...
written 6 months ago by nia0
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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 6 months ago by nia0 • updated 6 months ago by svlachavas570
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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 6 months ago by nia0
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microarray analysis code
... hello fellows , i am currently working on a project in which i have to do micro array analysis.I am working on R for analysis, my series have 10 samples and it is normalized so i directly applied limma code on that. The code is working but i am not satisfied with the result or with my code .kindly ...
microarray written 6 months ago by nia0
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TF ANALYSIS USING JASPAR
... Dear fellows,   firstly i identified degs using LIMMA dataset provide 1065 probeids with relevant info. from which i select 260 genes (no specific reasons ) 105 was up-reg and 155 was down-reg then i do func. enrichment using genecodis3  where i submit 260 genes and i got around 90 GO molecular fun ...
transcription jaspar written 7 months ago by nia0 • updated 7 months ago by James W. MacDonald45k
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Comment: C: phenotypic data and (.cel) file
... Thankyou James it works i need one more help.  i want to identify and retrieve all DEGs from the data and  set the p value<0.05 and fdr<0.01  how can i do this? " The limma package in R wasused to identify DEGs. Altered expression of probes was determined using t-tests, and theBenjamini-Hoch ...
written 7 months ago by nia0
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Comment: C: Error in GEOquery
... Why don't you donwload it manually by searching your gse id and then download raw data by clicking http , download soft files and matrix file as well . other than that try this code may be this work for you. this is the method for downloading soft files: library(GEOquery) gse <- getGEO('GSE67 ...
written 7 months ago by nia0
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Comment: C: phenotypic data and (.cel) file
... so if  i do the LIMMA step directly so how to get the entrez id in up and down annotated table. library(affy) library(affycoretools) d1<-ReadAffy() pData(d1)<-read.table(“pd.txt",row.names=1,header = T,sep="\t"); pData(d1) d1 library(limma) pData(d1)[,1 ] group<- factor(pData(d1)[,1 ], ...
written 7 months ago by nia0

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