all variables in design formula must be columns in colData (Deseq2) error
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Galina • 0
@91fadf4e
Last seen 2 days ago
Slovakia

Good day,

Please help with batch option in Deseq2, I have the error below and can't understand the problem as for me my METADATA_RAT has nessesary columns

txi.salmon_rat ENSRNOG00000000070 1.276541e+02 1.296898e+02 1.332189e+02 1.133108e+02 1.110791e+02 1.381127e+02 ENSRNOG00000000073 3.887378e+01 4.370201e+01 4.711458e+01 3.889587e+01 3.678910e+01 4.497496e+01 ENSRNOG00000000075 7.934947e+01 6.401462e+01 6.494397e+01 8.041880e+01 7.816325e+01 7.012191e+01....

coldata_rat <- data.frame(batch = as.factor(METADATA_RAT$batch)) METADATA_RAT$batch [1] "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" [8] "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" .....

dds_rat_with_batch <- DESeqDataSetFromTximport(txi.salmon_rat, colData = coldata_rat, design = ~ batch + condition) Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData

Could you please help with it,

Galina

BatchQC batchinDeseq2. columnsincolData. • 311 views
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ATpoint ★ 4.2k
@atpoint-13662
Last seen 23 hours ago
Germany

Your code is poorly readable. Suggest you select and then highlight with markdown using the 10101 button.

Generally, colData(dds) must have all the columns you reference in design. Here, it is only batch. condition is missing.

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Thank you for advice, you mean I need to add:

countdata_rat <- data.frame(condition = as.factor(METADATA_RAT$treatment))

and total:

dds_rat_with_batch <- DESeqDataSetFromTximport(txi.salmon_rat, colData = coldata_rat, countData = countdata_rat, design = ~ batch + condition)

?

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coldata_rat <- data.frame(conditions=..., batch=...)
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thank you!

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Good day ATpoint,

Could you pls advise also ehy this error could happened

design contains one or more variables with all samples having the same value, remove these variables from the design

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