I want to do a time course analysis with maSigPro ,i seen the manual but still im not clear what kind of data it can use ,is it the tophat protocol output that can be used? Like the final cuffdiff analysis can be used ? But it seems that it contains data of replicates that mean it can take cufflink input ?
Any input or suggestion would be highly appreciated
A package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data. Updated maSigPro writingdaddy.com best writing services supports RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. maSigPro was developed to treat continuous microarray intensities and applies LMs to model gene expression.
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version 2.3.6
this not what i was looking for
I think I sort of understand what are the major steps a maSigPro pipeline, but I am still struggling with the kind of data, which is expected for an RNA-seq experiment. The user's guide (https://www.bioconductor.org/packages/devel/bioc/vignettes/maSigPro/inst/doc/maSigProUsersGuide.pdf) has a section on NGS, but I am still confused about the terminology used there. There is this "counts" argument to distinguish between an NGS and microarray expriment - but are also row counts (that would be non-normalized data) provided as an input? The manual also says: "Data must be normalized before the application of maSigPro as it is not integrated any normalized method." That to me, implies e.g. RPM or RPKM values rather than raw counts. Taken together, I would say: "counts = TRUE" for an NGS experiment and normalized ata as input. Is my interpretation right?
I am new to the NGS and large data world and an input from someone, who already run the analysis successfully would be welcomed. Thanks in advance!