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Search: Posts Made By: KYR
Forum: Bioinformatics 05-19-2015, 01:04 PM
Replies: 1
Views: 2,701
Posted By KYR
Lightbulb How to use combat in R??

I'm trying to use combat to correct for batch effect in our dataset. The sample csv files contains genes in rows, and samples in columns, and expression values are from different microarray. We have...
Forum: Epigenetics 10-10-2014, 03:23 PM
Replies: 1
Views: 1,369
Posted By KYR
Can anyone recommend a software for finding DMRs in Chipseq?

We have a dataset of aligned and normalized data (originally from chipseq methylation) and we'd like to find DMRs.

I thought of USeq, though our data are already normalized so I'm not sure where...
Forum: Bioinformatics 10-10-2014, 10:06 AM
Replies: 0
Views: 1,200
Posted By KYR
Smile Which software/algorithm do you use to find DMR in chipseq methylation data?

I'm fairly new in the CHIP-seq field and would like to have recommendation on the best way to find DMRs.

Which software/platform/algorithm do you use (and why) to find differentially methylated...
Forum: Bioinformatics 08-01-2014, 06:42 PM
Replies: 4
Views: 5,374
Posted By KYR
Question Thanks for your answer. I use mcols() to...

Thanks for your answer. I use mcols() to double-check that the comparison is done as I need it, i.e.,

Ctrl vs T
Ctrl vs B
Ctrl vs A

I still don't understand if, despite what mcols says, the...
Forum: Bioinformatics 07-28-2014, 12:03 PM
Replies: 4
Views: 5,374
Posted By KYR
Exclamation [DESeq2] Multiple replicates, multiple treatments

I'm experiencing issues again with the replicates of our experiment. We should be comparing 3 types of treatments in one heatmap.


Ctrl vs T
Ctrl vs B
Ctrl vs A


Each of which have 3...
Forum: RNA Sequencing 07-16-2014, 01:50 PM
Replies: 13
Views: 4,122
Posted By KYR
Uhh indeed we have duplicated gene names, we have...

Uhh indeed we have duplicated gene names, we have to investigate before proceeding further. Thanks for your answers :)
Forum: RNA Sequencing 07-16-2014, 01:39 PM
Replies: 13
Views: 4,122
Posted By KYR
That's what I've done originally, but it gave me...

That's what I've done originally, but it gave me the following error:

> mydata4 = read.table("matrix4.txt", header=TRUE, row.names=1)
Error in read.table("matrix4.txt", header = TRUE, row.names =...
Forum: RNA Sequencing 07-16-2014, 01:32 PM
Replies: 13
Views: 4,122
Posted By KYR
yes that's what's happening here, the first...

yes that's what's happening here, the first column gene symbol should be row.names. Though I don't know how to fix that. Any help would be greatlly appreciated.. :)
Forum: RNA Sequencing 07-16-2014, 01:29 PM
Replies: 13
Views: 4,122
Posted By KYR
I gives me the following: >...

I gives me the following:

> dim(as.matrix(mydata4))
[1] 25197 10

I guess I have one more row column because of the gene symbol column which is first and should be row.names.
Forum: RNA Sequencing 07-16-2014, 01:16 PM
Replies: 1
Views: 1,621
Posted By KYR
Exclamation DESeq2 - COLUMN and ROWS number don't match

I have a table of count of control (3 replicates), treatment B (3 replicates) and treatment A (3 replicates). The first column is the gene symbol, table is as below:

Gene_symbol C1 C2 C3 B1 B2 B3...
Forum: RNA Sequencing 07-16-2014, 12:59 PM
Replies: 13
Views: 4,122
Posted By KYR
Exclamation Indeed, I started again from a fresh R command...

Indeed, I started again from a fresh R command shell, and that error doesn't appear anymore. However it generates another one:



library( "DESeq2" )
library("Biobase")
mydata =...
Forum: RNA Sequencing 07-16-2014, 12:15 PM
Replies: 13
Views: 4,122
Posted By KYR
Exclamation Need help with DESeq2

I have a text file, containing read counts per gene for each treatments and control, with the following column

[Gene Symbol] [C1] [C2] [C3] [B2] [B3] [A1] [A2] [A3]
C is Control
A is Treatment...
Forum: Bioinformatics 07-15-2014, 10:55 PM
Replies: 3
Views: 3,565
Posted By KYR
Exclamation DESeq2 error in data.frame (multiple treatments and multiple replicates)

I have a text file, containing read counts per gene for each treatments and control, with the following column

[Gene Symbol] [C1] [C2] [C3] [A1] [A2] [A3] [B1] [B2] [B3]


C is Control
A is...
Forum: Bioinformatics 06-26-2012, 09:24 PM
Replies: 0
Views: 1,795
Posted By KYR
Exclamation Samtools Error Message : no @SQ lines in the header

I have the same issue with samtools no matter how hard I'm trying to grab the header it just doesn't work ..

samtools view -H file.bam > header.sam
samtools reheader header.sam header.unique.bam...
Forum: Bioinformatics 05-28-2012, 04:50 PM
Replies: 2
Views: 895
Posted By KYR
Thanks! Yeah actually samtools is much more...

Thanks! Yeah actually samtools is much more faster than Bowtie. I wanted to do a denovo alignment with Bowtie after selecting a few reads of the mitochondrial chromosomes, so I thought that I needed...
Forum: Bioinformatics 05-28-2012, 12:27 AM
Replies: 2
Views: 895
Posted By KYR
Exclamation How to search reads with Bowtie ?

We did an alignment with BWA and have 4 BAM files. How can I filter only mt reads with Bowtie ?
Forum: Core Facilities 05-20-2012, 09:24 PM
Replies: 2
Views: 2,262
Posted By KYR
Your sequencer should have its own room in a...

Your sequencer should have its own room in a particle-free area, with a private door and / or double door to enter. The temperature of the room shouldn't be over 20 or 25 .. I'm not sure about that...
Forum: Bioinformatics 05-20-2012, 09:14 PM
Replies: 0
Views: 1,802
Posted By KYR
CNVnator : Error message Please Help!

I typed the following in unix and at step 3 CALCULATING STATISTICS CNVnator output an error message.. I have no clue what does it mean..

Here is what I typed :

./cnvnator -genome mm9 -root...
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