User: Saroj K Mohapatra

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Posts by Saroj K Mohapatra

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Comment: C: Bioconductor Digest, Vol 87, Issue 10
... Earlier you mentioned downloading the data from ArrayExpress. That should have the probe annotation file. Another option is to download the annotation file from the chip manufacturer's web site. For example: I am investigating the array express entry E-MEXP-2620. The Array design file from http://w ...
written 9.0 years ago by Saroj K Mohapatra400
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Comment: C: Bioconductor Digest, Vol 87, Issue 10
... Hi Avinash: You could create a vector using c(), e.g., if the first 3 are control and last 3 are cancer, then, > myclassvec <- c(0,0,0,1,1,1) For creating the gene name matrix, I hope you have the probe annotation file in which each probe (or probe set, for affy) is listed along with gene n ...
written 9.0 years ago by Saroj K Mohapatra400
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Answer: A: Bioconductor Digest, Vol 87, Issue 10
... Hi Avinash: I have never used hopach. But as the vignette suggests, you could get the information from the documentation for golub data. > require(hopach) > ?golub gives me the details of golub data: ----------------------- golub package:hopach R Documentation Gene expression dataset fr ...
written 9.0 years ago by Saroj K Mohapatra400
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Answer: A: Reg: GSEA
... Hi Rohit: Using the GOstats you can test for both over and under representation of GO terms using Hypergeometric test. There is a vignette "How To Use GOstats Testing Gene Lists for GO Term Association". Best wishes, Saroj Rohit Farmer wrote: > Hello everyone ... > > I just did a moder ...
written 9.1 years ago by Saroj K Mohapatra400
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Answer: A: how to generate a data frame containing all the coefficients of the different co
... Hi Benoit: > I tried the functions write.fit and topTableF but, with the first one > I cannot have the adjusted p-values ?write.fit ... Usage: write.fit(fit, results=NULL, file, digits=3, adjust="none", method="separate", F.adjust="none", sep="\t", ...) ... adjust: character string sp ...
written 9.2 years ago by Saroj K Mohapatra400
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Answer: A: Heatmap: row labels &amp; dendogram
... Hi Daniela: Glad that it helped. Daniela wrote: > Hi Saroj, > Many thanks for your answer. > Your pdf idea works very well though it kicks out the key, > even when I write key=T. > I am just guessing that you used keysize parameter (perhaps the same value I used, i.e., 0.1?) If so, ...
written 9.2 years ago by Saroj K Mohapatra400
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Answer: A: Heatmap: row labels & dendogram
... Hi Daniela: danieladna wrote: > Hi, > A two questions about heatmap.2 : > > What is the best approach to make the row labels readable? > Right now they are merging. I plotted 104 genes. The command cexRow > is not giving me the desired result, since the font size > needs to be ...
written 9.2 years ago by Saroj K Mohapatra400
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Answer: A: what does mean of Densities on y axis in the graph generated by plotDensities
... Hello Neeraj: The help command '?plotDensities' provides a description: Plots the densities of individual-channel intensities for two-color microarray data. Internally it uses the density() function to construct an estimate of the probability density function underlying the data. Basically, it dis ...
written 9.3 years ago by Saroj K Mohapatra400
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Comment: C: Which application to start BioConductor?
... Hi, I do not know if you already saw this: http://www.bioconductor.org/GettingStarted Extensive information carefully categorized. Saroj cihan inan wrote: > Well I am a biology student at university. and next year I will be a master > student. I am planning to be in bioinformatics departmen ...
written 9.4 years ago by Saroj K Mohapatra400
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Answer: A: Hello,I have very urgent questions
... Dear Wei: The message indicates some problem with memory. You need a machine with more memory. You might also try with smaller data (e.g., fewer microarrays, etc.) and see if the problem persists. There are functions that get the Gene Ontology annotation for genes in the org.xx.eg.db packages, whe ...
written 9.6 years ago by Saroj K Mohapatra400

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