User: mschmidt

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mschmidt0
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Posts by mschmidt

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Comment: C: Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns er
... Dear Michael, that's much easier way! Thanks! It looks that I was unable to generate `dds` because I multiplied TPM matrix by 1e+6 what produced too much counts. Best regards, Marcin ...
written 3 months ago by mschmidt0
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Comment: C: Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns er
... Yes, I have a TPM matrix. It has 45946 rows but with NAs (empty cells replaced later by NAs). the data columns have different number of NAs. I can split the matrix into separate files but I do not know the number of mapped reads per sample. I have Summary of the expression results for this experime ...
written 3 months ago by mschmidt0
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Comment: C: Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns er
... Thanks for fast reply, I was testing several setups of the tximport for last several minutes. I have single file with 15 columns (Tx, Gene.Name, and 13 columns named by tissues with TPMs) I used: txi <- tximport(file = "data4pcatxi.tsv", type="none", txOut = TRUE, + txId ...
written 3 months ago by mschmidt0
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Comment: C: Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns er
... I found this example to test with: df=data.frame("treat"=sample(c(80:100),6, replace=FALSE), "treat1"=sample(c(90:103),6, replace=FALSE), "treat2"=sample(c(80:100),6, replace=FALSE), "ctrl"=sample(c(60:90),6, replace=FALSE), ...
written 3 months ago by mschmidt0
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Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
... I want to explore RNAseq data from Expression Atlas (EMBL-EBI database). The dataset downloaded from the database was in TPM, so I changed NAs into '0's and multiplied the values by 1E+6 (to get integer values) and added 1 for later log-transformation data4PCA[is.na(data4PCA)] = 0 data4PC ...
deseq2 rlog written 3 months ago by mschmidt0 • updated 3 months ago by Michael Love26k

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