User: Agaz Hussain Wani
Agaz Hussain Wani • 260
- Reputation:
- 260
- Status:
- Trusted
- Location:
- India
- Last seen:
- 1 year, 2 months ago
- Joined:
- 4 years, 2 months ago
- Email:
- h************@yahoo.com
A research scholar currently working in the area of Bioinformatics on gene expression data analysis. I have a post graduation in computer science with computer applications as a specialization. I am Interested to study biological data and design tools and techniques with the aim of identifying potential cancer biomarkers.
Posts by Agaz Hussain Wani
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Comment:
C: Processing agilent data by limma
... Thank you very much for the answer. I tried reading the exon arrays from GSE32006 seprately,
raw_data <- read.maimages(pdata[,1], source = "agilent", green.only = TRUE)
but I get the same issue
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
Specified column headings n ...
written 14 months ago by
Agaz Hussain Wani • 260
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... I am trying to process Agilent data by using limma R package. For GSE10469, I used the following code
raw_data <- read.maimages(pdata[,1], source = "agilent") # pdata file is having group information
I get the error:
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
Specifi ...
written 14 months ago by
Agaz Hussain Wani • 260
• updated
14 months ago by
Gordon Smyth ♦ 37k
1
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...
Check topTable without setting the limit for p.value and lfc. I am sure that you have no significant genes on p.value = 0.05 and lfc = 2. You can also check by increasing the limit of p.value.
...
written 14 months ago by
Agaz Hussain Wani • 260
0
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... P-values of a sample like we do with
pvalue <- assayData(data.mas5calls)[["se.exprs"]]
I am not interested to compare two or more groups (and I know that I can do with limma), But what I am interested is shown in the example code.
...
written 15 months ago by
Agaz Hussain Wani • 260
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... Thank you I got it by affy::rma(). And please ignore the above comment. Is it possible to get p-values?.
...
written 15 months ago by
Agaz Hussain Wani • 260
0
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...
Thank you for your comment. But when I do that using RMA
file <- ReadAffy(filenames = file.choose())
rma(file)
I get an error Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’
...
written 15 months ago by
Agaz Hussain Wani • 260
0
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2
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... I use readCodelink() to get feature names. I have updated my question, please check the edit.
...
written 15 months ago by
Agaz Hussain Wani • 260
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... Confusing thing is that Spot_mean is missing and I think Codelink package needs Spot_mean, raw or normalized data to generate expression values and SNR, though not sure. I check with other types also such as "Raw" and "Norm", but no benefit. I have shown some lines of the sample above.
...
written 15 months ago by
Agaz Hussain Wani • 260
2
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2
answers
304
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... I was trying to process CodeLink UniSet Rat I Bioarray data from GSE59913. Previously I have processed UniSet Human 20K I Bioarray using Codelink R package by the following code.
codset = readCodelinkSet(filename = codelinkpath[[i]])
features <- readCodelink(codelinkpath[[i]]) ## An additio ...
written 15 months ago by
Agaz Hussain Wani • 260
• updated
15 months ago by
Diego Diez • 730
1
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1
answer
470
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... I am trying to process data from Affymetrix HT HG-U133+ PM Array Plate GSE27544 by using affy R package. I am interested to generate the expression values, present/absent calls and p-values. I am using the following code
# read file
file <- ReadAffy(filenames = file.choose())
eset.mas5 = ma ...
written 15 months ago by
Agaz Hussain Wani • 260
• updated
15 months ago by
Guido Hooiveld • 2.5k
Latest awards to Agaz Hussain Wani
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Agilent data processing by Limma R package
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For How to prepare targets.txt file in codelink.
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Meta-analysis of gene expression data by 'MetaDE'
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Annotating codelink data file
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: How to access vector of certain column in phenotype data.
Scholar
3.2 years ago,
created an answer that has been accepted.
For A: How to access vector of certain column in phenotype data.
Student
3.2 years ago,
asked a question with at least 3 up-votes.
For Can i set a path for readCodlinkSet()
Student
3.2 years ago,
asked a question with at least 3 up-votes.
For Annotation package for Codelink 55K Human Array
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: How to access vector of certain column in phenotype data.
Rising Star
4.0 years ago,
created 50 posts within first three months of joining.
Autobiographer
4.1 years ago,
has more than 80 characters in the information field of the user's profile.
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