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cris12gm / normSeq

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Reporting job error here: S291BWFLFRG9M3N #5

Closed emilyyaklich closed 1 year ago

cris12gm commented 1 year ago

Dear @emilyyaklich ,

Sorry for the inconvenience, we have checked the job ID and fixed it, please see the results here: https://arn.ugr.es/normSeq/results/?jobID=S291BWFLFRG9M3N

The problem was on the input annotation file, which was not tab-separated, please check that for future jobs.

Best, Cristina

emilyyaklich commented 1 year ago

Hi Cristina,

Thank you for your reply - this makes sense! I do have another question, for the Remove Unwanted Variation - RUVs method it is mentioned on the input page that the annotation file must contain a third column with replicate annotation - what is meant by this?

Emily

On Mon, Aug 28, 2023 at 5:53 AM Cristina Gómez-Martín < @.***> wrote:

Dear @emilyyaklich https://github.com/emilyyaklich ,

Sorry for the inconvenience, we have checked the job ID and fixed it, please see the results here: https://arn.ugr.es/normSeq/results/?jobID=S291BWFLFRG9M3N

The problem was on the input annotation file, which was not tab-separated, please check that for future jobs.

Best, Cristina

— Reply to this email directly, view it on GitHub https://github.com/cris12gm/normSeq/issues/5#issuecomment-1695391578, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKPYV4X3HEU2E77NJHV2P5DXXRTBJANCNFSM6AAAAAA35FF2A4 . You are receiving this because you were mentioned.Message ID: @.***>

cris12gm commented 1 year ago

Dear Emily,

To perform the RUV method, the annotation file must contain a third column, like in the example below, where all samples that are replicates of one condition, have the same label. In the example below, there are 3 replicates of "cerebellum", and all of them are labeled as "Cerebellum" and 2 replicates of "cortex", and all of them are labeled as "Cortex". It must be also tab-separated.

sample group replicate Cerebellum_1 CNS Cerebellum Cerebellum_2 CNS Cerebellum Cerebellum_3 CNS Cerebellum Cortex_1 CNS Cortex Cortex_2 CNS Cortex

XiaoweiKI commented 1 year ago

There was error in NormSeq job ID 7ORUOUEENHB8BLU. Would you please check? Thanks!

cris12gm commented 1 year ago

Dear @XiaoweiKI ,

Sorry for the inconvenience, we have checked the job ID and fixed it, please see the results here: We https://arn.ugr.es/normSeq/results/?jobID=7ORUOUEENHB8BLU

The problem was on the matrix file, which contained some duplicated rows. We optimized the website so from now on that shouldn't be a problem.

Best, Cristina