DESeq deal with 426 samples

[wbb1813]

Hi guys,

I analysis the TCGA data which have 426 samples with DESeq in R, after run about 3h ,then occur a error which is about files to big and more than 3GB, so both PC and server are all can not calculate it. But when I only user 6 samples,it works well , so my question is how can I use DESeq to deal with 426 samples?

thanks!

[dpryan]

You'd be better off with DESeq2. Also, I thought that TCGA didn't provide raw counts.

[wbb1813]

Sure, I will try to use DESeq2. I download TCGA data from firehose and the file name is raw_count but not all numbers is integer, so I transform it into integer then I can use DESeq, Actually I don't know why they are not integer.

[dpryan]

I recall them being RSEM expected counts or something like that. You might just log2 transform them and then use limma, which is likely more appropriate for non-count values.

[Gordon Smyth]

The RSEM expected counts are "count-like", so better to run them through voom and into the limma pipeline rather than log2 transforming. This will be quite fast even for 426 samples.

[wbb1813]

Voom and limma is a good way to deal with this data , thank you for your reply!