I have RNA -seq data from the HiSeq with 2 normal and 2 diseased replicates (a total of 4 samples). I tried both DESeq and PARTEK GS to obtain differentially expressed genes. However, I see very different results.
I saw the following discussion:
and have read about both the tools and understand that both are workign differently. However, I am still not sure which one would be better to understand the expression changes.
For Partek, I used a 2-way anova (condition & replicates) on the RPKM values.
For DESeq I provide counts using HtSeq in the suggested order and perform the analysis following the documentation.
I would really appreciate any suggestions on this.
I saw the following discussion:
and have read about both the tools and understand that both are workign differently. However, I am still not sure which one would be better to understand the expression changes.
For Partek, I used a 2-way anova (condition & replicates) on the RPKM values.
For DESeq I provide counts using HtSeq in the suggested order and perform the analysis following the documentation.
I would really appreciate any suggestions on this.
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