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rosedu1 / deconvSeq

deconvolution for RNAseq and bisulfite sequencing
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Does normalized expression data work well? #6

Open yingyonghui opened 3 years ago

yingyonghui commented 3 years ago

Thanks for your amazing tool for deconvolution of bulk seq data. I now just want to deconvolute the TCGA bulk data based on a scRNA-seq reference data, and I have only the normalized expression data in log scale. I'm wondering whether deconvSeq work well when applied on the normalized input data?

Many thanks! Yonghui

rosedu1 commented 3 years ago

Yonghui, Currently, deconvSeq does not work on microarray data. We may update it to add that in a future version. Rose

yingyonghui commented 3 years ago

Yonghui, Currently, deconvSeq does not work on microarray data. We may update it to add that in a future version. Rose

Hi @rosedu1 , Thanks for your quick reply! I'm new to the filed, and I thought that the TCGA bulk data come from RNA-seq, not microarray. And am I wrong?

Best, Yonghui

rosedu1 commented 3 years ago

Yonghui, Sorry about the confusion, I was answering another email that came to me at the same time as yours. decovnSeq is based on count data so you cannot use normalized data with it. You can go to https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 and obtain the raw read counts for TCGA instead. Rose