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Przemol / seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
http://przemol.github.io/seqplots
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Problems about normalization between datasets for profile plot #16

Closed pengyu1608 closed 8 years ago

pengyu1608 commented 8 years ago

I drawed profile plot for five datasets. The inputed bigWig file were created by HOMER and total tag counts were normalized to 1e7. In the profile plot, I noticed the baseline of 5 datasets were quite different (see below). I wonder how the normalization within SeqPlots is done? testprofileplot

Przemol commented 8 years ago

Hi pengyu1608,

SeqPlots does not normalize the signal by default and plots values directly obtained from track file. However, you can use Transform signal option in Guide lines and data scaling tab to log2 transform or z-score (the mean and standard deviation are calculated based only on plotting ranges, not the whole track) your signal. z-score transform would make the baselines match on the plot.

pengyu1608 commented 8 years ago

Thanks for the explanation.

Best, Peng

yup@pku.edu.cn

From: Przemol Date: 2016-10-31 20:24 To: Przemol/seqplots CC: Peng Yu; Author Subject: Re: [Przemol/seqplots] Problems about normalization between datasets for profile plot (#16) Hi pengyu1608, SeqPlots does not normalize the signal by default and plots values directly obtained from track file. However, you can use Transform signal option in Guide lines and data scaling tab to log2 transform or z-score (the mean and standard deviation are calculated based only on plotting ranges, not the whole track) your signal. z-score transform would make the baselines match on the plot. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

pengyu1608 commented 8 years ago

Hi, Przemol:

I have a question about clustering part of seqplots. Could it be possible to export the clustering result (i.e. relationship of genes to cluster)? It will be very helpful. Thanks.

From: Przemol Date: 2016-10-31 20:24 To: Przemol/seqplots CC: Peng Yu; Author Subject: Re: [Przemol/seqplots] Problems about normalization between datasets for profile plot (#16) Hi pengyu1608, SeqPlots does not normalize the signal by default and plots values directly obtained from track file. However, you can use Transform signal option in Guide lines and data scaling tab to log2 transform or z-score (the mean and standard deviation are calculated based only on plotting ranges, not the whole track) your signal. z-score transform would make the baselines match on the plot. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Przemol commented 8 years ago

Just click "Cluster indicates" in the bottom left. Hore on the clustering result here: http://przemol.github.io/seqplots/#getting-pdfs-and-cluster-info image

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