Commit b780951c authored by AntonieV's avatar AntonieV
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descriptions for report for deseq2 pca, volcano, ma and scatter plot and for...

descriptions for report for deseq2 pca, volcano, ma and scatter plot and for fingerprint and profile plot and for heatmap
parent 1345df8a
**`MA plot <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.plotMA>`_ (FDR 0.01)**
shows the log2 fold changes versus the mean of normalized counts from
`DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false
discovery rate (FDR) threshold of 0.01 for all samples of each antibody. For more information about DESeq2 please see
`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
**Volcano plot (FDR 0.01)** shows the significance (adjusted p-value) versus the log2 fold changes of the results of the
`DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false
discovery rate (FDR) threshold of 0.01 for all samples of each antibody. For more information about DESeq2 please see
`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
**`MA plot <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.plotMA>`_ (FDR 0.05)** shows the log2 fold changes versus the mean of normalized counts from `DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false discovery rate (FDR) threshold of 0.05 for all samples of each antibody. For more information about DESeq2 please see `documentation https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html`_.
**Volcano plot (FDR 0.05)** shows the significance (adjusted p-value) versus the log2 fold changes of the results of the
`DESeq2 <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf>`_ analysis filtered on a false
discovery rate (FDR) threshold of 0.05 for all samples of each antibody. For more information about DESeq2 please see
`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
**`PCA plot <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.plotPCA>`_
(Principal Component Analysis)** describes variance of the
`rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
`vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
`DESeq2 <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_ analysis with regard to
the antibody used. For more information about DESeq2 please see
`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
**Scatter plots** uses the matrix of the
`rlog <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.rlog>`_ or
`vst <https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf#Rfn.vst>`_ transformed counts from
`DESeq2 <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_ analysis for each sample
to compare them in paired combinations. For more information about DESeq2 please see
`documentation <https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html>`_.
**deepTools `plotFingerprint <https://deeptools.readthedocs.io/en/latest/content/tools/plotFingerprint.html>`_** is a
quality control tool, which determines how well the signal in the ChIP-seq sample can be differentiated from the
background distribution of reads in the control sample. plotFingerprint randomly samples genome regions of a specified
length and sums the per-base coverage that overlap with those regions. These values are then sorted according to their
rank and the cumulative sum of read counts is plotted. With a perfect uniform distribution of reads along the genome and
infinite sequencing coverage a straight diagonal line is shown in the plot. For more information on the interpretation of
the plots please see `here <https://deeptools.readthedocs.io/en/latest/content/tools/plotFingerprint.html#what-the-plots-tell-you>`_.
For more information about plotFingerprint metrics see
`here <https://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html>`_.
**deepTools `plotHeatmap <https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html>`_** creates a
heatmap for scores over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the samples.
The `scores <https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html>`_ represent the signal over a
set of regions where all regions are scaled to the same size.
**deepTools `plotProfile <https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html>`_** creates a
profile plot for scores over sets of genomic regions and gives a visualisation for the genome-wide enrichment of the
samples. The `scores <https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html>`_ represent the
signal over a set of regions where all regions are scaled to the same size.
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