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Search: Posts Made By: alisrpp
Forum: Bioinformatics 02-17-2014, 11:53 AM
Replies: 1
Views: 4,069
Posted By alisrpp
Hi ChrisAU, Did you solve your problem? I am...

Hi ChrisAU,

Did you solve your problem? I am now having the same issue and I could use a little bit of help.

Thanks!
Forum: Bioinformatics 01-17-2014, 12:11 PM
Replies: 5
Views: 2,967
Posted By alisrpp
And how can I do that?

And how can I do that?
Forum: Bioinformatics 01-16-2014, 01:11 PM
Replies: 5
Views: 2,967
Posted By alisrpp
Hi swbarnes2, What I am trying to do is to...

Hi swbarnes2,

What I am trying to do is to perform some differential gene expression analyses with DESeq2 just using those transcripts above 1000bp. In order to do that I need to filter the...
Forum: Bioinformatics 01-13-2014, 10:38 AM
Replies: 5
Views: 2,967
Posted By alisrpp
How to filter a SAM/BAM file by bp

Hi community,

I want to filter my SAM/BAM files to just keep my transcripts above 1000bp. What I am doing now is to convert my SAM/BAM files into fasta and then filter them but then I have...
Forum: Bioinformatics 10-24-2013, 09:12 AM
Replies: 123
Views: 48,812
Posted By alisrpp
Hi, I'm using DESeq2_1.2.0 and I am having...

Hi,

I'm using DESeq2_1.2.0 and I am having this error:

> resSig <- res[ res$padj < .1, ]
Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE, exact = FALSE) :
subscript contains...
Forum: Bioinformatics 10-22-2013, 02:33 PM
Replies: 123
Views: 48,812
Posted By alisrpp
Ups! Thanks! By using: ...

Ups! Thanks!

By using:

browseVignettes("DESeq2")

i am obtaining

/library/DESeq2/doc/DESeq2.pdf not found
Forum: Bioinformatics 10-22-2013, 12:38 PM
Replies: 123
Views: 48,812
Posted By alisrpp
Here is my sessionInfo() > sessionInfo() R...

Here is my sessionInfo()

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
...
Forum: Bioinformatics 10-21-2013, 08:06 PM
Replies: 123
Views: 48,812
Posted By alisrpp
Hi Michael, First of all, thank you for all...

Hi Michael,

First of all, thank you for all the help.

I tried fitType="mean" with the code:

#Count matrix input
Cele_SPvsLR = read.csv (file.choose(), header=TRUE, row.names=1)
CeleDesign...
Forum: Bioinformatics 10-21-2013, 08:04 AM
Replies: 123
Views: 48,812
Posted By alisrpp
Hi, By doing what you suggested: dds<-...

Hi,

By doing what you suggested:

dds<- estimateSizeFactors(dds)
ddsMean <- estimateDispersions(dds, fitType="mean")
ddsMean <- nbinomWaldTest(ddsMean)
plotDispEsts(ddsMean)

I'm obtaining...
Forum: Bioinformatics 10-17-2013, 04:25 PM
Replies: 123
Views: 48,812
Posted By alisrpp
This is my dispersion plot, is not exactly like...

This is my dispersion plot, is not exactly like in the manual... so i don't know what to think.
Can you give me your opinion, please?

Thanks,
Forum: Bioinformatics 10-16-2013, 01:35 PM
Replies: 123
Views: 48,812
Posted By alisrpp
Now i'm getting this error: Warning...

Now i'm getting this error:

Warning messages:
1: glm.fit: algorithm did not converge
2: In estimateDispersionsFit(object, fitType = fitType, quiet = quiet) :
parametric fit failed, trying...
Forum: Bioinformatics 10-16-2013, 01:04 PM
Replies: 123
Views: 48,812
Posted By alisrpp
Done! I updated R and now is working perfecly. ...

Done! I updated R and now is working perfecly.
Thanks Michael!
Forum: Bioinformatics 10-16-2013, 10:13 AM
Replies: 123
Views: 48,812
Posted By alisrpp
Sure! > traceback() 14: get(name, envir =...

Sure!

> traceback()
14: get(name, envir = asNamespace(pkg), inherits = FALSE)
13: methods:::.setDummyField
12: (function (value)
{
if (missing(value))
`.->data`
...
Forum: Bioinformatics 10-16-2013, 09:57 AM
Replies: 123
Views: 48,812
Posted By alisrpp
Hi, I'm new in DESeq2 and i'm having...

Hi,

I'm new in DESeq2 and i'm having problems to create my dds.

I have a matrix with eXpress results (read counts) with 2 conditions (SP, EB) and 2 replicates/condition.

This is what i'm...
Forum: Bioinformatics 10-15-2013, 11:09 AM
Replies: 8
Views: 5,205
Posted By alisrpp
Significant up-regulated and downregulated genes with DESeq

Hi,

I'm trying to identify the significant up-regulated and down-regulated genes in 6 different moments of the life cycle of "my" animal.

I have 11 libraries (2 replicates/stage, except for one...
Forum: Bioinformatics 06-05-2013, 12:15 PM
Replies: 5
Views: 2,846
Posted By alisrpp
I'm still generating the same plot, any ideas...

I'm still generating the same plot, any ideas about how to interpretate it?

Thanks.
Forum: Bioinformatics 05-28-2013, 01:31 PM
Replies: 5
Views: 2,846
Posted By alisrpp
Hi, I'm using DESeq version 1.10.1

Hi,

I'm using DESeq version 1.10.1
Forum: Bioinformatics 05-28-2013, 12:53 PM
Replies: 5
Views: 2,846
Posted By alisrpp
Hi Muthu, I'm trying to run your suggestion:...

Hi Muthu,

I'm trying to run your suggestion:



and this is what is happening to me:

> cds <- estimateDispersions( cds,
+ method="pooled",
Forum: Bioinformatics 05-28-2013, 11:23 AM
Replies: 5
Views: 2,846
Posted By alisrpp
DESeq - estimateDispersion doubt

Hi,

I'm using DESeq for the first time and at the step of variance estimation i'm obtaining very different plots from the manual and i have no idea about how to interpretate them.

My data are:...
Forum: Bioinformatics 05-27-2013, 12:04 PM
Replies: 9
Views: 1,798
Posted By alisrpp
Hi all, I discovered that the problem was...

Hi all,

I discovered that the problem was that RSEM was generating (for some reason that i cannot explain) decimal number in the column of expected count where you are suppose to have only integer...
Forum: Bioinformatics 05-24-2013, 02:44 PM
Replies: 9
Views: 1,798
Posted By alisrpp
> colSums(spercysts_vs_embryos) C4 ...

> colSums(spercysts_vs_embryos)
C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11
17856472 4152157 27308366 3531719
Forum: Bioinformatics 05-24-2013, 01:56 PM
Replies: 9
Views: 1,798
Posted By alisrpp
> tail(spercysts_vs_embryos) ...

> tail(spercysts_vs_embryos)
C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11
comp99965_c0_seq1 3 0 11 0
comp99972_c0_seq1 0 0 ...
Forum: Bioinformatics 05-24-2013, 01:55 PM
Replies: 9
Views: 1,798
Posted By alisrpp
Sorry Simon, i was desperate...

Sorry Simon, i was desperate...
Forum: Bioinformatics 05-24-2013, 01:08 PM
Replies: 9
Views: 1,798
Posted By alisrpp
Unhappy DESeq no recognizing row.names

Hi,

I'm trying to use DESeq to know the differential expressed genes of my datasets and i'm encountering that DESeq is not recognizing my row.names so i can't create my cds.

My .csv input file...
Forum: Bioinformatics 01-29-2013, 11:33 AM
Replies: 2
Views: 3,887
Posted By alisrpp
Eliminate rRNA contamination with Bowtie

Hi,

I'm working with Illumina 101bp reads of marine sponges. Before trimming the adapters and filtering by quality with the Trimmomatic i run FastQC to check, among other things, the amount of...
Showing results 1 to 25 of 40

 


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