Help with how to interpret density plot (cummeRbund)

[DonDolowy]

Dear all,

I am analyzing my 50bp paired-end RNA-seq using the Tophat - Cuffdiff - Cufflinks - cummeRbund pipeline.

I am a little confused on how to interpret the density plot I get from one experiment, where I am comparing ESC, Haploid and Diploid cells.
For the RP sample, I do not see this bimodal distribution, as I see for the other samples.



Is it something I should worry about? I have kind of same shape with another couple of samples from white adipose tissue. My boss flags the normalization as crap as soon as he doesnt see the bimodal distribution, but I am not really sure if it really has to be bimodal. What are your thoughts on this?

The fastqc files pass the fastQC quality controls.

Thanks in advance. Appreciate all inputs!

[jp.]

Did you get the answer ?
If yes, can you explain me please ?
Thanks

[jp.]

Hi
I got something for you but not very useful.

commands:
# this will generate same figure as yours
> csDensity(genes(cuff_data), logMode=TRUE, pseudocount= 0, features=FALSE, replicates=FALSE)
# try changing pseudocount = ? i.e 1 to 0.000001 to -1
csDensity(genes(cuff_data), logMode=TRUE, pseudocount= -1, features=FALSE, replicates=FALSE)

you can get the results as you want. But I dont know if it is the way to do it and not sure how to explain it. I just tried.
Do reply plz

Dear all,

I am analyzing my 50bp paired-end RNA-seq using the Tophat - Cuffdiff - Cufflinks - cummeRbund pipeline.

I am a little confused on how to interpret the density plot I get from one experiment, where I am comparing ESC, Haploid and Diploid cells.
For the RP sample, I do not see this bimodal distribution, as I see for the other samples.



Is it something I should worry about? I have kind of same shape with another couple of samples from white adipose tissue. My boss flags the normalization as crap as soon as he doesnt see the bimodal distribution, but I am not really sure if it really has to be bimodal. What are your thoughts on this?

The fastqc files pass the fastQC quality controls.

Thanks in advance. Appreciate all inputs!

[DonDolowy]

No, I never got an explanation but since I posted here I have analyzed data from many other experiments, where I usually do not run see such a density plot.

[jp.]

You may try it out my above commands and you will get normalised good view.
If you need more info about heatmap and color change and incuding dandogram such thing, plz do reply
Thank you

No, I never got an explanation but since I posted here I have analyzed data from many other experiments, where I usually do not run see such a density plot.