User: Manisha Brahmachary

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9 years, 4 months ago
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11 years, 8 months ago
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m*****@c2b2.columbia.edu

Posts by Manisha Brahmachary

<prev • 8 results • page 1 of 1 • next >
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Problem with extracting subset of samples for 500K in aroma affymetrix
... Hello, If anybody in this forum uses the aroma affymetrix, I will be very obliged if you can help me with this query: I am doing an unpaired copy number analysis with 500K arrays using the CRMAv2. I want to use a subset of my samples the reference, instead of the all the samples as robust average f ...
written 9.3 years ago by Manisha Brahmachary80 • updated 9.3 years ago by James W. MacDonald51k
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need advice with creating an eSet with a different type of phenodata
... I am trying to create an eSet with the following data structures: pdata is: ABCB7 ABCC1 ABCC4 ABCD1 ABCD3 ABCD4 ABCE1 ABCF1 ABCG1 ABHD14A ABHD14B ABHD2 ABHD4 ABHD5 ABHD8 ABL2 X1015 2 2 2 2 2.00 2 2 2.00 2.00 2.00 2.00 2 2 2.00 2 2 X1238 2 ...
written 10.3 years ago by Manisha Brahmachary80 • updated 10.3 years ago by Sean Davis21k
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Comment: C: problem installing affycoretools in R in linux environment
... I also tried installing biomaRt separately but I was not able to do that. How do I get around this problem? Please see the session below: biocLite("biomaRt") Running biocinstall version 2.1.11 with R version 2.6.1 Your version of R requires version 2.1 of BioConductor. Warning in install.packages( ...
written 11.1 years ago by Manisha Brahmachary80
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problem installing affycoretools in R in linux environment
... I am having problems installing affycoretools in R (2.6) on my linux environment. When I do the same thing with my R (2.6) in windows I donot have any such problem and it gets properly installed. I will appreciate any suggestion on how to install it in linux environment I am trying to install aff ...
go affycoretools written 11.1 years ago by Manisha Brahmachary80 • updated 11.1 years ago by James W. MacDonald51k
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query about RNA degradation plot
... Hello, Can anyone suggest me how I can include a legend showing all the samples that are plotted on a RNA degradation plot that is part of simpleaffy/ affy package? Thanks manisha [[alternative HTML version deleted]] ...
written 11.2 years ago by Manisha Brahmachary80 • updated 11.2 years ago by Jenny Drnevich1.9k
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filter gene based on cv
... I am using coefficient of variation as a way of filtering affymetrix data and I am new to using this method for filtering data: I have a query based on the genefilter package. Does this command: x <-filterfun(cv(0.5)) mean removing genes that have a coefficient of variation of more that ...
genefilter written 11.4 years ago by Manisha Brahmachary80 • updated 11.4 years ago by James W. MacDonald51k
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how to import mas5 data into expresso (affy package)
... Hello, I will be be obliged if someone can reply to this query: I have a question related to expresso and limma package. I have mas5.0 normalized data and I do not have the raw .CEL files. I want to use limma on the mas5.0 data to find differentially expressed genes. I read in the journ ...
microarray limma process affylmgui written 11.4 years ago by Manisha Brahmachary80 • updated 11.4 years ago by James W. MacDonald51k
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within class standard deviation query
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080304/ 713afd38/attachment.pl ...
written 11.7 years ago by Manisha Brahmachary80 • updated 11.7 years ago by James W. MacDonald51k

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