User: neeraj rana

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neeraj rana60
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Posts by neeraj rana

<prev • 6 results • page 1 of 1 • next >
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Comment: C: [maSigPro] two color array analysis of time series in different cell lines.???
... hi jim, thanks for your response to query. As i understood from tutorial min.obs is used for gene expression value(minimum expression value).But as i am using fold change (M=R\G) instead of expression value so the fold change will be in negative also for down regulated genes.So i passed the value i ...
written 6.0 years ago by neeraj rana60
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[maSigPro] two color array analysis of time series in different cell lines.???
... I want to use maSigPro package for cell line data treated at different time points. i have three cell lines(HF,HT,NLT),treated on 3 time points separately(1,4,12hrs). I want to make comparison (HF vs HT),(HF vs NLT),(HT vs NLT). I am using M value for comparison produced by limma after normalization ...
limma masigpro written 6.0 years ago by neeraj rana60 • updated 12 months ago by sbbinfo900
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Limma normalizeBetweenArrays does not normalize M values using Quantile method directly.???
... Hi dear all, I am using limma for two color Agilent Microarray analysis. I found that normalizeBetweenArrays does not perform Quantile normalization directly to the M values. For that reason i had to use the following command MA_Quantile<- noralizeBetweenArrays(*MA$M*,method="quantile") To norma ...
microarray limma written 6.0 years ago by neeraj rana60 • updated 6.0 years ago by James W. MacDonald51k
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Comment: C: Agilent two color Quantile normalization
... thanks jim But when i use normalizeBetweenArrays(MA,methode="quamtile),it is supposed to perform quantile normalization on M values and the mean ,median,maximum value and minimum value should be the same of all arrays after normalization. I am copying my script here for reference. > targets < ...
written 6.0 years ago by neeraj rana60
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Agilent two color Quantile normalization
... Dear Bioconductor List, I am doing two color Agilent microarray analysis by limma. I tried to normalize* M *values by using following command.But both the commands are giving different M values. *(1) MA<- normalizeBetweenArrays (MAw, method="quantile") * *(2) MA <- **normalizeBetweenArrays ...
microarray limma written 6.0 years ago by neeraj rana60 • updated 6.0 years ago by James W. MacDonald51k
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Vector for Targest in Tquantile Normalization for different groups.
... Dear List, I am doing one microarray analysis. I need to perform Tquantile Normalization for different groups.For that i need to make one vector to define groups. Here is my analysis. y.q <- normalizeBetweenArrays(y, method="Tquantile",targets="*how to make targets vector here??*") > targets ...
microarray written 6.2 years ago by neeraj rana60 • updated 3.9 years ago by Gordon Smyth38k

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