We would like to be able to download and compare outcomes from several tools using the same in-put datasets (initially Affy datasets then Illumina and Agilent chip and finally RNAseq data). Publicly accessible, open source tools would be most useful. Thanks. Bob.
I would suggest bioconductor. It is open source and is commonly used for microarray and RNAseq analysis. In particular the limma package can do both. It requires a bit of learning, however.
http://www.bioconductor.org/
http://www.bioconductor.org/packages/release/bioc/html/limma.html
are you asking how to correlate the various platform data? for example taking affy and agilent and see i.e. which genes show the same pattern?
Hi, Bob
I have discussed your questions with our bioinformatics expert who is collaborating with me on several genome-wide analysis projects. I will forward his suggestions to your email. Please check your email when you have time. Best. Kevin
"Yes - looking to compare expression patterns across platforms...Bob"
if you don't want to get into the learning curve of using limma the simplest way of doing it is to calculate pairwise correlation and build a linear model per each pair, i.e. affy vs agilent, agilent vs rnaseq, rnaseq vs affy.
if you are familiar with R you can use the lm() function using the average expression of each experimental condition. I'd still suggest to check the distribution of the data before starting since RNA seq data tend to be heavily squelched towards the left. to partially correct this you can transform the data by using either log2, box-cox transformation or inverse hyperbolic sine function (as "log(x+sqrt(x^2+1))) prior building the linear model
Sebastiano,
As you're probably aware limma uses linear models, but has methods to normalise the data prior to fitting. This is critical as without normalisation microarray data is not comparable. Likewise for RNAseq. Fortunately, limma also has the voom function to normalise RNAseq data.
Although limma doesn't assume a negative binomial distribution that many other RNAseq tools do, (edgeR, DESeq) a log-normal is close enough for all but the most lowly expressed genes.
Dear Robert Clarke Affymetrix Expression Console: Free software from Affymetrix that can be used to analyze Affymetrix microarray data. Expression Console includes functionality for mapping Affymetrix data to other platforms, including: MAS 5.0 Chip Definition File (CDF): CDF files map probe sequences to genes or gene transcripts. Affymetrix provides a variety of CDF files, including files for different species and tissue types. Platform Mapping Files: Platform Mapping Files map Affymetrix probe IDs to probe IDs on other platforms. Affymetrix provides a variety of platform mapping files, including files for Agilent, Illumina, and Qiagen platforms.
Anything else?
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