User: Hernando Martínez

Reputation:
100
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New User
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Last seen:
9 years, 5 months ago
Joined:
9 years, 6 months ago
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h**********@gmail.com

Posts by Hernando Martínez

<prev • 10 results • page 1 of 1 • next >
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removal of probes called "Absent"
... Hi, I am trying to remove probes called A (absent) in all my microarray samples. I am trying to get the p-values for the probes across all samples so I can use genefilter to create a mask and select the present genes. However, I get the following error: > data<-ReadAffy() > rawcalls<-ma ...
probe genefilter written 9.4 years ago by Hernando Martínez100 • updated 9.4 years ago by Iain Gallagher930
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removal of genes with low expression values
... Hi, I need to remove genes with low expression values from a expression matrix. I would like to remove those with an average of expression values less than a certain cut-off. I was thinking in computing the average for each row, create a list with the gene names for which their average is less than ...
written 9.4 years ago by Hernando Martínez100 • updated 9.4 years ago by Robert Castelo2.3k
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Network plot
... Hi list, I am working with a network, in a table form like this: Gene1 Gene5 0.76 Gene1 Gene79 0.89 Gene2 Gene8 0.97 ... Basically, each row represents two genes that interact, and their pearson correlation coefficient (from 0.7 to 1). What I want to get is a plot r ...
network written 9.4 years ago by Hernando Martínez100 • updated 9.4 years ago by Sean Davis21k
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common genes in different platforms
... Hi, I am trying to compare differentially expressed genes between normal and control in two data sets. The problem is that each data set uses a different array platform, and I want to work only with those genes that are common to both datasets. Is there any function in R to do that? Many thanks, -- ...
written 9.5 years ago by Hernando Martínez100 • updated 9.4 years ago by Wolfgang Huber13k
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selection of dif.exp.genes defining FDR in SAM
... Hi, I am using SAM to identify differentially expressed genes in a set of microarrays, but I want to select a value of False Discovery Rate for the cut-off instead of using the delta. Does anyone know which parameter to introduce to do so? Or any function to get the delta for a specific FDR? Thank y ...
written 9.5 years ago by Hernando Martínez100 • updated 9.5 years ago by Holger Schwender900
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Comment: C: R memory limit
... Thank you all very much. For the moment I can analyze the data using R64. However, I need to analyse as well a bigger matrix, to maybe I will need the other proposed solutions as well. Again, thanks, you have been very helpful. Hernando 2010/6/14 Kasper Daniel Hansen > If you're on a mac and ...
written 9.5 years ago by Hernando Martínez100
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Comment: C: R memory limit
... sorry, I am trying to analize an expression microarray of nearly 350 samples. My R version is R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How do I load R in 64 bit? (maybe this is a trivial question for you but it is not for me, as I have no computer background). Thank you very much again, Herna ...
written 9.5 years ago by Hernando Martínez100
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R memory limit
... Hi, I am working with large data, and when I try to read it into R using 'ReadAffy', I get the following error message: "cannot allocate a vector size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been reading some posts online, but I haven't found a clear solution. Maybe is a limit in R, ...
written 9.5 years ago by Hernando Martínez100 • updated 9.5 years ago by Benilton Carvalho4.3k
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Comment: C: unique values for repeated geneIDs
... Thank you very much Sean, I have been working with function aggregate and it is exactly what I need. However, there is still a painful detail that I cannot get rid of. I hope you can help me too with this. I have this text file: A B C D d1 2 23 2 d1 4 22 2 d1 5 24 2 d2 10 7 2 d2 20 8 3 d1 7 23 2 d3 ...
written 9.5 years ago by Hernando Martínez100
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unique values for repeated geneIDs
... Hello everyone, my name is Hernando, and I am new to R. I have a little problem that maybe you can help me with, as I have been looking through the packages with no success, and it shouldn't be very difficult to solve. I have a text file containing a list of genes, with expression values for each al ...
microarray written 9.5 years ago by Hernando Martínez100 • updated 9.5 years ago by Sean Davis21k

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Popular Question 9.4 years ago, created a question with more than 1,000 views. For removal of genes with low expression values

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