Error in if (var(data.matrix[i, cond2[[j]]]) == 0) { : missing value where TRUE/FALSE needed

[widsquid]

Hello, thanks for the great package. I successfully went through the demo but am having some trouble with my data.

batchQC(counts, batch = batch, condition = cond, interactive = TRUE)
Error in if (var(data.matrix[i, cond2[[j]]]) == 0) { :
missing value where TRUE/FALSE needed

One clue is that my many of my conditions have only one replicate. Does this only work if there are multiple reps per condition (for all conditions)?
Thanks so much.

[mani2012]

Hi, Yes, otherwise there is no batch effect to study for that condition. Best, Mani From: widsquid ***@***.***> Sent: Thursday, November 11, 2021 7:24 PM To: mani2012/BatchQC ***@***.***> Cc: Subscribed ***@***.***> Subject: [mani2012/BatchQC] Error in if (var(data.matrix[i, cond2[[j]]]) == 0) { : missing value where TRUE/FALSE needed (Issue #24) Hello, thanks for the great package. I successfully went through the demo but am having some trouble with my data. batchQC(counts, batch = batch, condition = cond, interactive = TRUE) Error in if (var(data.matrix[i, cond2[[j]]]) == 0) { : missing value where TRUE/FALSE needed One clue is that my many of my conditions have only one replicate. Does this only work if there are multiple reps per condition (for all conditions)? Thanks so much. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#24>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACMB4PADAQPPZIBT2I7LTSLULRNATANCNFSM5H3UR3BQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[widsquid]

Ahh yes of course, thanks so much for the reply. Is there any way around this? For example, if I am trying to normalize for batch effect across ~600 RNA-seq samples that were collected from a series of 8 experiments (batches) where each condition is present only once with the exception of 8 (pos and neg ctrl) conditions which were replicated in each batch. Is there any way to use the information from the 8 samples that appear across all batches to extrapolate a batch correction to the entire set of conditions? Thanks again.
W

[mani2012]

You may have to analyze the batch excluding those single sample conditions first and then use the batch effect information when analyzing those single sample conditions. Best, Mani From: widsquid ***@***.***> Sent: Sunday, November 14, 2021 9:32 PM To: mani2012/BatchQC ***@***.***> Cc: Solaiappan Manimaran ***@***.***>; Comment ***@***.***> Subject: Re: [mani2012/BatchQC] Error in if (var(data.matrix[i, cond2[[j]]]) == 0) { : missing value where TRUE/FALSE needed (Issue #24) Ahh yes of course, thanks so much for the reply. Is there any way around this? For example, if I am trying to normalize for batch effect across ~600 RNA-seq samples that were collected from a series of 8 experiments (batches) where each condition is present only once with the exception of 8 (pos and neg ctrl) conditions which were replicated in each batch. Is there any way to use the information from the 8 samples that appear across all batches to extrapolate a batch correction to the entire set of conditions? Thanks again. W — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#24 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACMB4PA4WNFYXNOVZ77ZAPLUMBWIPANCNFSM5H3UR3BQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.