what does negative value mean in gene expression profile?

Question

[modarzi]

hi,

I would like to use data series in GEO by GSE71120. In this dataset in addition raw data(SRA) in a supplementary file as GSE71120_Expression_RNAseq_41_FFPE_sarcomas.tsv.gz. in that data, you find sample title as columns and gene symbol as rows. based on this explanation I have to preprocess raw data which needs more time or "GSE71120_Expression_RNAseq_41_FFPE_sarcomas.tsv.gz" file. my problem is I can't understand why some values for gene expression is negative in GSE71120_Expression_RNAseq_41_FFPE_sarcomas.tsv.gz file.

I appreciate if anybody solves my problem.

[Kevin Blighe]

Hey, I do not believe that file contains raw counts.... The data processing steps indicate that they are Cufflinks-derived estimated abundances. See here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1827506

[modarzi]

Dr. Blighe, Thanks for your comment. I know that "GSE71120_Expression_RNAseq_41_FFPE_sarcomas.tsv.gz" is not raw data. my problem is why some expression values for some genes are negative? because after getting count file we have to normalize expression values. but in the data processing steps, I can't find any description for the normalization process. I sent an email for Frédéric Chibon the Contact person of GSE71120. he answered me just by this sentence: "Data are Log". I know in RNA-seq we have to logFold Change but why some values are negative. could you please explain to me why some values are negative in "GSE71120_Expression_RNAseq_41_FFPE_sarcomas.tsv.gz"?

Thanks

[Kevin Blighe]

Frédéric's response, although short and imprecise, explains why there are negative values in the data that you download. For that study, you should try to obtain the raw data so that you can process it yourself.

[modarzi]

Dear Dr Blighe I understood why some values are negative. I want to use this data for my analysis. Minimum of this data is "-9.965784" and a maximum of that is 12.11787. In my study I shouln't have negative values. does it make sense that I add "9.965784" to all myExprdata values? based on this decision, the minimum value of myExprdata will be zero and I can use it for my study. I appreciate if you share your comment with me.

[Kevin Blighe]

On the log scale, values can be negative:

log2(4)
[1] 2

log2(2)
[1] 1

log2(1)
[1] 0

log2(0.5)
[1] -1

log2(0.25)
[1] -2

log2(0.125)
[1] -3