User: rohit

gravatar for rohit
rohit30
Reputation:
30
Status:
New User
Location:
India
Last seen:
3 years, 9 months ago
Joined:
4 years, 10 months ago
Email:
r**************@gmail.com

Posts by rohit

<prev • 9 results • page 1 of 1 • next >
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Functional Classification of genes
... Dear all, I have a list of 200 genes which I have obtained from microarray analysis. I want to classify them on the basis of their function whether some of them are involved in cell proliferation, cell migration and differentiation .   How can I perform this functional classification of these genes ...
functional classification written 3.9 years ago by rohit30 • updated 3.7 years ago by EagleEye6.4k
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Comment: C: Analysing Microarray Data In Bioconductor
... Dear Obi, I have normalized my affymetrix microarray data and did gene filter to remove probes that do not have entrez id's. Now I want to annotate my data for gene symbols. I've followed your steps to retrieve gene symbols. After writing the data in text file I found a column mentioning as <S4 ...
written 3.9 years ago by rohit30
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identification of single pathway from microarray data
... Hi everyone, I have analysed affymetrix microarray. After normalizing and removing duplicate entrez id's I'm left with approximately 17,000 genes. I want to know that out of these 17,000 genes which genes lies in a particular pathway which is of my interest and how to get each gene's involvement i ...
pathways softwares microarray R written 3.9 years ago by rohit30 • updated 3.9 years ago by Chris Evelo10.0k
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Analysing illumina micro array
... Hello everyone, I am tasked with analysing the gene expressions from illumina microarray. I've downloaded illumina raw data and non- normalized data from GEO  having accession number GSE31738. In the raw data folder I couldn't find any text file having Average signal, BEAD_STDERR and Average NBEADS ...
non normalized R illumina written 3.9 years ago by rohit30 • updated 3.9 years ago by andrew.j.skelton735.8k
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gene filtering for agilent microarray using Limma
... Hello everyone, I'm analysing agilent microarray data using limma package. I want to do gene filter to remove the probes that do not give any expression values. Is there any workflow to filter genes in limma package? Thank you in advance. ...
agilent microarray gene filtering limma R written 3.9 years ago by rohit30 • updated 10 months ago by Kevin Blighe45k
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Comment: C: Retrieving Probe To Gene Ids For Affymetrix Chips In Bioconductor
... I'm getting error while using for affymetrix chips of hgu133plus2 annotation. when I write normalized mapped data to file I can see symbol names, probe ID's, entrez ID's but not expression values. The expression values column is displaying as "<S4 object of class "ExpressionSet">". can you ple ...
written 4.1 years ago by rohit30
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Comment: C: how to remove sequence names and probe names from normalized agilent micro array
... Thank you Franco for your suggestion. I have imported the file into excel and deleted the undesired columns. ...
written 4.1 years ago by rohit30
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how to remove sequence names and probe names from normalized agilent micro array data
... hello everyone, I'm analyzing the agilent microarray data using limma package. I have performed normalization using y <- normalizeBetweenArrays(y,method="quantile") now I need to get the normalized gene expression values. I have used the command  write.table(y, file="Tt.txt", sep="\t", quote= ...
agilent R limma written 4.1 years ago by rohit30 • updated 4.1 years ago by Antonio R. Franco4.1k
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how to find over representation of TFBS for a specific gene
... hello everyone, I want to identify the over represented TFBS families in the promoter region of cancer specific genes. The promoter sequence i took is -3Kb upstream to TSS and +1Kb downstream to TSS. Can anyone please tell me are there any online tools or data bases for the identification of over r ...
tfbs families gene over representation written 4.9 years ago by rohit30

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