Timeline for Error in cor(exprs(gse), use = "c") : no complete element pairs
Current License: CC BY-SA 4.0
9 events
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| Oct 18, 2020 at 20:10 | comment | added | user3051 | @user432797 You typically download the fastq files either from NCBI or ENA. Check sra-explorer.info which can search and provide download links for datasets. I also wrote a (today a bit deprecated given sra-explorer exists) tutorial that might be interesting, see biostars.org/p/325010 It is not recommended imho to directly download files via fasterq-dump, that is often unstable in my experience. The tutorial covers recommended approaches, or simply use the download links from-sra.explorer.info to get fastq right away (my preferred approach). | |
| Oct 18, 2020 at 19:45 | comment | added | Bastian Schiffthaler |
The recommended way to download these runs from the SRA is to use the SRA toolkit, specifically the program fasterq-dump from it. See here for the How-to. Basically, just run fasterq-dump <RUN ACCESSION>. E.g.: fasterq-dump SRR9606476 for the first run of you experiment. Download the SRA toolkit here
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| Oct 18, 2020 at 19:42 | comment | added | Bastian Schiffthaler | On the bottom of the GEO page, you see the "Relations" category, which points to NCBI BioProject PRJNA551397. There, under "project data", you see "SRA experiments". Click on the number 28, which takes you to the sequence read archive page for the samples. Now click on Send to run selector | |
| Oct 18, 2020 at 19:23 | comment | added | user432797 | I want to do both from raw data and FPKM @ATpoint, how and where to get the raw fastq data? | |
| Oct 18, 2020 at 19:19 | vote | accept | user432797 | ||
| Oct 18, 2020 at 16:15 | comment | added | user3051 | You cannot use GSE data here. It is for microarray as I said above. Download raw data (fastq, this is NGS not array), and then align them. If you are new to this then simply use the FPKM that are provided. | |
| Oct 18, 2020 at 15:28 | comment | added | user432797 | How do you process the data of GSE in this case? I looked for questions that have the same kind of data, but I couldn’t find any, what do you recommend @ATpoint ? | |
| Oct 18, 2020 at 10:18 | history | edited | user3051 | CC BY-SA 4.0 |
added explanation why code fails (empty obejct)
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| Oct 18, 2020 at 9:10 | history | answered | user3051 | CC BY-SA 4.0 |