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Search: Posts Made By: Marcos Lancia
Forum: Bioinformatics 04-11-2017, 08:05 AM
Replies: 1
Views: 1,143
Posted By Marcos Lancia
Question Calculating free energy in batch

Hi everyone, Im working with 3'-UTR and 5'-UTR sequences of a group of genes of interest. I'd like to calculate their free Gibbs energy in batch. I found a web tool called MFOLD...
Forum: Bioinformatics 01-18-2017, 09:12 AM
Replies: 2
Views: 1,342
Posted By Marcos Lancia
Thanks so much! That's exactly what I was looking...

Thanks so much! That's exactly what I was looking for! I know nothing about bioinformatic tools, so this kind of experiences are useful to learn something. Thanks again!
Forum: Bioinformatics 01-18-2017, 08:43 AM
Replies: 2
Views: 1,342
Posted By Marcos Lancia
Question How to calculate GC% in R?

Hi everybody, I'd like to know if there is a tool in R to calculate CG% content and G if it's possible too from a table with several genes. I have almost 300 genes and I have their sequences. I can...
Forum: Bioinformatics 01-10-2017, 11:49 AM
Replies: 1
Views: 1,358
Posted By Marcos Lancia
Question Looking for 3'-UTR and 5'-UTR sequences

Hi everyone! I have a question, I hope you can help me out. I have a list of genes that Id like to obtain their 5'-UTR and 3'-UTR sequences. I work with Medicago truncatula, and I have RNA-SEQ data...
Forum: Bioinformatics 01-28-2016, 10:57 AM
Replies: 1
Views: 1,080
Posted By Marcos Lancia
Question Converting a CuffData.db file into a .tabular or .csv or .xls

Hi everybody, I need some help here. Id like to convert the cuffData file that it come from the Galaxy service into a .tabular or ,scv or .xls. and work with ggplot2. How can I do that? Is it...
Forum: Bioinformatics 10-20-2015, 11:39 AM
Replies: 9
Views: 1,281
Posted By Marcos Lancia
Talking Done!

Yes! youre right again! I changed commas by dots and it worked!
Than you very much, I think Im loving you right now :D
Forum: Bioinformatics 10-20-2015, 10:00 AM
Replies: 9
Views: 1,281
Posted By Marcos Lancia
Hi again. Youre right. Mi data are "characters"...

Hi again. Youre right. Mi data are "characters" after reading the file as you suggested with fread. Numbers different from 0 are replaced with NAs.
Forum: Bioinformatics 10-20-2015, 05:08 AM
Replies: 9
Views: 1,281
Posted By Marcos Lancia
Exclamation Hi! Thanks for your help again. I figured it out...

Hi! Thanks for your help again. I figured it out that mi data were "factors" instead of "numerics". So, I did a transformation:

d1 <- read.csv("all filter1.csv", stringsAsFactors = FALSE,...
Forum: Bioinformatics 10-19-2015, 11:08 AM
Replies: 9
Views: 1,281
Posted By Marcos Lancia
I only plotted 2000 points. I dont think is a...

I only plotted 2000 points. I dont think is a dense packed points issue. It must be something else that I dont understand. Im just learning bioinformatics making errors, please be patient with me....
Forum: Bioinformatics 10-19-2015, 09:29 AM
Replies: 9
Views: 1,281
Posted By Marcos Lancia
Question Dark plot ???

Hi! I did a plot with some of my data and the plot was dark. Some ideas?

Commands were simple,

d1 <- read.csv("all filter1.csv", header=T)
plot(d1[,7], d1[,18])

Somebody knows how can I...
Forum: Bioinformatics 10-19-2015, 09:23 AM
Replies: 4
Views: 1,156
Posted By Marcos Lancia
Question Some ideas what is it?

Hi! I did a plot with some of my data and the plot was dark. Some ideas?

Commands were simple,

d1 <- read.csv("all filter1.csv", header=T)
plot(d1[,7], d1[,18])

Somebody knows how can...
Forum: Bioinformatics 10-16-2015, 12:47 PM
Replies: 4
Views: 1,156
Posted By Marcos Lancia
I tought about that, but I tought there were a...

I tought about that, but I tought there were a easiest way using a different command without losing information. Thanks for writing @dpryan!
Forum: Bioinformatics 10-16-2015, 11:59 AM
Replies: 4
Views: 1,156
Posted By Marcos Lancia
Question not memory size enough

Hi everybody, I need help with my big plot. I couldn't see my plot because an error appeared:
Error: cannot allocate vector of size 6.9 Gb
In addition: Warning messages:
1: In apply(x, margin,...
Forum: Bioinformatics 10-16-2015, 10:16 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Ok, thanks so much for your time. You helped me...

Ok, thanks so much for your time. You helped me so much. If you can read this, there's a problem with the %>%.
Error: could not find function "%>%"

The 2nd option you gave me deleted all data....
Forum: Bioinformatics 10-16-2015, 08:33 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Ok, my table is ready. Now, my problem is that I...

Ok, my table is ready. Now, my problem is that I have non-numerical data in my columns. How can I avoid that? For example,
plot(data$log2.FC.transcriptome., data$log2.FC.translatome.)

In...
Forum: Bioinformatics 10-16-2015, 08:00 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
I tried before with plot(d[,10], d[,24]), but it...

I tried before with plot(d[,10], d[,24]), but it says "error in evaluating the argument 'x' in selecting a method for function 'plot': Error in `[.data.frame`(d, , 10) : undefined columns selected"
...
Forum: Bioinformatics 10-16-2015, 07:53 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Ok! you're right. I changed the names of the...

Ok! you're right. I changed the names of the headers, but I crashed with a new problem. I have some non-numerical data in the columns, some are "inf" or "-inf". How can I avoid that?
Forum: Bioinformatics 10-16-2015, 07:28 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
I tried the same with ggplot, and the answer was...

I tried the same with ggplot, and the answer was the same.
Forum: Bioinformatics 10-16-2015, 07:16 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Arrow little advances

"log2(FC transcriptome)", and "log2(FC translatome)" are my headers that I want to plot. Theyre the 10th and 24th columns in my table.
Forum: Bioinformatics 10-16-2015, 07:11 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Im working with dpryan's commands. I could make...

Im working with dpryan's commands. I could make variable d, but when I tried plotting

plot(d$log2(FC transcriptome), d$log2(FC translatome))

but there's an error message saying
Error:...
Forum: Bioinformatics 10-16-2015, 06:32 AM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Hi people, thanks for writing. I'll check it out...

Hi people, thanks for writing. I'll check it out your ideas, I'll see how well I understand your commands.
Forum: Bioinformatics 10-15-2015, 01:56 PM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Oh, I'm sorry. I'm working on R. Thanks!

Oh, I'm sorry. I'm working on R. Thanks!
Forum: Bioinformatics 10-15-2015, 01:50 PM
Replies: 18
Views: 1,890
Posted By Marcos Lancia
Question Scatterplot of 2 columns

Hi everybody. I have a simple question for bioinformatics. Id like make a scatterplot of 2 of my columns from a table .csv or .tabular. How can I do that? Thanks!
Forum: Bioinformatics 05-08-2015, 11:18 AM
Replies: 15
Views: 4,370
Posted By Marcos Lancia
Hi, Your suggestion of plotting log(m[, ]+1)...

Hi,
Your suggestion of plotting log(m[, ]+1) gaves me an idea. I made the cor(log(m[, ]+1)) and it worked! The cor() values are up to 0.95 all of them. Thanks for your help, mission accomplished,...
Forum: Bioinformatics 05-05-2015, 10:38 AM
Replies: 15
Views: 4,370
Posted By Marcos Lancia
No, Im not working with Cole Trapnell datasets,...

No, Im not working with Cole Trapnell datasets, these data are mine.
Question: How can I be sure that data plotted are the same analyzed by correlation? Make some kind of matrix, maybe?
Thanks so...
Showing results 1 to 25 of 31

 


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